© ReutersSince Bo Xilai's downfall, his activities have come under immense media scrutiny
Citing "nearly a dozen people with party ties", it said the disgraced Mr Bo ran a wire-tapping network across Chongqing, where he was party chief.
His officials even listened to a phone call involving Hu Jintao, it said.
Chinese authorities have not mentioned wire-tapping in reports about Bo Xilai, whose wife is being investigated over the death of a British national.
They are investigating Mr Bo over "serious discipline violations", while his wife, Gu Kailai, has been detained as a suspect in the death of Neil Heywood, the British businessman found dead in Chongqing in November 2011.
Chinese authorities say they believe Mr Heywood was murdered.
Mr Bo - a high flier once expected to reach the top echelons of office - has not been seen in public since he was removed from his political posts, in the biggest political shake-up in China in years.
'Direct challenge'
Bo Xilai's wire-tapping operation began several years ago as part of an anti-crime campaign in Chongqing, the New York Times said.
It was handled by Wang Lijun, the police chief whose flight to the US consulate in February signalled the start of Mr Bo's downfall, and expanded into targeting political figures.
Last year, the paper reported, "operatives were caught intercepting a conversation between the office of Mr Hu and Liu Guanglei, a top party law-and-order official whom Mr Wang had replaced as police chief".
A conversation between Minister of Supervision Ma Wen, who was visiting Chongqing, and Mr Hu himself was also monitored, the paper said.
Authorities in Beijing found out and began investigating, straining the relationship between Mr Wang and Bo Xilai.
The wire-tapping "was seen as a direct challenge to central authorities", the newspaper reported, citing party insiders.
These new claims will add to the sense that this scandal has exposed deep rifts and mistrust at the very highest level of China's Communist Party, reports the BBC's Damian Grammaticas from Beijing.
Also important were fears that Mr Bo, seen as a divisive populist, could not be trusted if elevated to the highest levels in the party, our correspondent adds.
Bo Xilai's fall from grace comes with China due to begin its once-in-a-decade leadership change in October.
Since the scandal erupted, the lifestyle and political and business dealings of he and his family have come under intense media scrutiny.
His brother has resigned as director of a Hong Kong-based company, a day after his son issued a statement defending his lifestyle.
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