© BBCKenyan farmers say genetically modified crops threaten their survival
They were protesting at reports that Kenya would lift its restrictions on GM crops following a recent drought, leading to maize shortages.
The demonstrators said they believed a shipment had already arrived and feared it could contaminate the soil.
Kenyan millers want to import cheap GM maize to cope with the shortages.
The BBC's Odhiambo Joseph in Nairobi says the protesters included farmers and environmentalists.
"The importation of GM maize is a ploy by leading millers to kill us - the small-scale farmer," protester Gacheke Gachihi said.
The march was organized by the African Biodiversity Network and the Unga Revolution.
'Toxic product'
They said a consignment of GM maize from South Africa was in the port city of Mombasa, waiting to be off-loaded.
They wanted it destroyed or sent back, the protesters said.
The chairman of the Kenyan parliament's agriculture committee, John Mututho, confirmed to the BBC that the GM maize was at the port.
He said he would lead a delegation of parliamentarians to Mombasa next week to inspect the consignment.
"We are totally opposed to this toxic product," Mr Mututho said.
The Kenyan government approved a law last year to import GM products.
However, this was subject to the state-run National Biosafety Authority (NBA) giving its go-ahead.
'First for country'
Roy Mujiira from the NBA said the body now intended to give the green light.
"We are targeting to publish the regulation by next week, and it is a first for the country," he told Reuters news agency.
Kenya is facing an acute maize shortage, caused by a prolonged drought.
Millers have been lobbying the government to allow them to import GM maize, saying it would help end the shortage and lower prices.
"GM maize is cheaper by about 30% compared with non-GM maize," Diamond Lalji, the chairman of Kenya's Cereal Millers Association, told Reuters.
The government recently dropped tariffs on maize imports in order to curb a sharp rise in prices.
African countries have been under pressure from the pro-GM lobby, led by the US, to grow GM crops to reduce hunger.
South Africa farms GM maize, but there is strong resistance to it in many other African countries.
Supporters of GM crops say they boost production and require less fertilizer and pesticides.
Comment: Supporters of Genetically Modified crops say these crops boost production and require less fertilizer and pesticides but the opposite has been scientifically researched in the following book Failure to Yield: Evaluating the Performance of Genetically Engineered Crops
The biotechnology industry has been promising better yields since the mid-1990s, but Failure to Yield documents that the industry has been carrying out gene field trials to increase yields for 20 years without significant results.
In addition to evaluating genetic engineering's record, Failure to Yield considers the technology's potential role in increasing food production over the next few decades. The report does not discount the possibility of genetic engineering eventually contributing to increase crop yields. It does, however, suggest that it makes little sense to support genetic engineering at the expense of technologies that have proven to substantially increase yields, especially in many developing countries. In addition, recent studies have shown that organic and similar farming methods that minimize the use of pesticides and synthetic fertilizers can more than double crop yields at little cost to poor farmers in such developing regions as Sub-Saharan Africa.
"If we are going to make headway in combating hunger due to overpopulation and climate change, we will need to increase crop yields," said Gurian-Sherman. "Traditional breeding outperforms genetic engineering hands down."
Opponents say more scientific data is needed, arguing that their long-term genetic impact on humans and wildlife could be harmful.
In 2002, Zambia rejected GM food aid in the midst of a food crisis affecting some three million people.
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