Police have confirmed the death of David Kato and say they have arrested one suspect.
Uganda's Rolling Stone newspaper published the photographs of several people it said were gay next to a headline reading "Hang them".
Homosexual acts are illegal in Uganda, with punishments of 14 years in prison.
The BBC's Joshua Mmali, in Kampala, says it is unclear whether the death is linked to the Rolling Stone campaign but police have said there is no connection between Mr Kate's activism and his death.
The police say that though they have arrested one suspect, the main suspect - who they say lived with Mr Kato - remains on the run.
An MP recently tried to increase the penalties to include the death sentence in some cases.
Death threats
There has been a recent spate of "iron-bar killings" in Mukono, where Mr Kato lived, in which people have been assaulted with pieces of metal.
Witnesses have told the BBC that a man entered Mr Kato's home near Kampala, and beat him to death before leaving.
His Sexual Minorities Uganda (Smug) group said Mr Kato had been receiving death threats since his name, photograph and address were published by Rolling Stone last year.
Frank Mugisha, the group's executive director, told the BBC's Network Africa programme he was "devastated" on hearing the news from New York.
"He was killed by someone who came in his house with a hammer, meaning anyone else could be the next target."
Mr Mugisha said Mr Kato had recently been concerned about the threats he had received.
Human Rights Watch (HRW) has called for a swift investigation into his death.
"David Kato's death is a tragic loss to the human rights community," said HRW's Maria Burnett.
He had campaigned against the Anti-Homosexuality Bill, which appears to have been quietly dropped after provoking a storm of international criticism when it was mooted in 2009.
US state department spokesman PJ Crowley said the US was "horrified and saddened" by Mr Kato's death and urged Ugandans to reject homophobic views.
"The US calls on the Ugandan authorities to actively investigate his murder and bring the perpetrators to justice," he said.
'Extra caution'
Following a complaint by Mr Kato and three others, a judge in November ordered Rolling Stone to stop publishing the photographs of people it said were homosexual, saying it contravened their right to privacy.
Several activists said they had been attacked after their photographs were published.
Mr Mugisha called on the Ugandan government to step up security for gay people.
"We're strongly asking every gay and lesbian and bisexual and transgender person in Uganda to watch out for their security ... [they] should take extra caution."
Rolling Stone editor Giles Muhame told Reuters news agency he condemned the murder and that the paper had not wanted gays to be attacked.
"There has been a lot of crime, it may not be because he is gay," he said.
"We want the government to hang people who promote homosexuality, not for the public to attack them."
"Iron-bar killings" were common in Uganda when former leader Idi Amin was in power in the 1970s.
A rapid response police team has been sent to the area and several suspects have been arrested over the killings.
David Kato
Uganda, My Heart Weeps for You!
A GLOBAL AUTHOR'S RESPONSE TO THE PROPOSED LEGISLATIVE GENOCIDE IN UGANDA -- by Terry Angel Mason
Uganda, Uganda, my heart weeps for you! For you kill, murder, and imprison the innocent (those who express love differently) in the name of The Righteous One, but it is clear that you do not know Him!
Like America, you label them pedophiles and child molesters, yet continue to close your eyes to the true heterosexual offenders, allowing them to continually rape your children and infect them with AIDS; men who foolishly believe that this will cure them from the pandemic.
It has been said that you freed yourself from the tyranny and oppression of a king (Mwanga) who was demented, greedy, self-serving and who defiled the people and if these things be true, then this is good! But you forgot that even though he was said to be corrupt and accused of raping the people both physically and emotionally for years, still we must judge each human being by their own conduct, character, and deeds, and not punish the innocent for another's sins.
Uganda, Uganda, my heart weeps for you because even though the rain falls frequently upon your land in the south and beautiful lakes run through your northern region, they have not cleansed you from your transgressions for you are still blinded by hatred, fear, and intolerance, and cannot see that the sun rises upon the just and the unjust, so that all men may be wooed to the Creator by love and mercy and not by hatred and discrimination!
For hundreds of years other nations robbed you of your wealth, stole your children and carried them away to foreign lands and enslaved them. Even today, in many regions of your country you suffer from extreme poverty because of usury and exploitation from men who lusted after your riches, saw you could not defend yourself, and carried them away to distant lands.
You must be very careful lest the handwriting of God also appear in judgment for your offenses and likewise be written upon your walls and inscribed in your Constitution now laced with fear and intolerance, having been saturated by the influence of misguided, self-seeking American Evangelists, these words spoken by the prophet Daniel: "MENE, MENE, TEKEL, UPHARSIN" The interpretation:
"God has numbered your kingdom, and finished it; TEKEK: You have been weighed in the balances, and found wanting; PERES: Your kingdom has been divided, and given to another!"
Thousands of you marched in your city streets to rid yourself of a sin that you say will most certainly bring the judgment of Sodom and Gomorrah upon your land; but like the Scribes and the Pharisees of Jesus' day, legalism and an incorrect interpretation of the Holy Scriptures have blinded you.
Because of your hatred for what you do not understand, The Prince of Darkness deceives you yet again; prostituting you like the demented king you managed to free yourself from decades ago; have you still not heard the words of Jesus who said, "He was a murderer from the beginning?"
Uganda, Uganda, my heart weeps for you! Don't you know that you cannot kill the innocent, batter and abuse your children, and lock them away in dungeons of cruelty for life simply because you refuse to accept who they really are without the very King of the Universe (whom you claim you worship), championing their cause, and lifting his righteous hand of justice and judgment against you?
He has heard the voices of the children devastated by earthquakes and disaster in Chile, Mexico and Haiti and He has freed the oppressed in America from hundreds of years of discrimination. He has even delivered the Jews from the oppression of a mighty pharaoh (once thought invincible) in Egypt. Surely, He will not turn a deaf ear to innocent same-gender-loving people in your country, nor allow you to murder them without cause and your land and your people not be judged for doing so!
Uganda, Uganda, I alone do not weep, "FOR A VOICE WAS HEARD IN RAMAH, WEEPING AND GREAT MOURNING, RACHEL WEEPING FOR HER CHILDREN; AND SHE REFUSED TO BE COMFORTED, BECAUSE THEY WERE NO MORE!" (Matthew 2:18)
by Terry Angel Mason, Global Author
WWW.TERRYANGELMASON.COM