The rights group says that since 28 November the Kenyan police have conducted three large raids and made "dozens of arbitrary arrests," detaining refugees from Ethiopia, Somalia, Sudan, and the Democratic Republic of Congo.
Thirteen people - mostly Kenyans - were killed in a suicide bomb attack on an Israeli-owned hotel near Mombasa on 28 November. Almost simultaneously, two ground-launched missiles narrowly missed an Israeli charter jet as it was taking off from Mombasa.
The authorities "have made no official link between the Mombasa attacks and this group of detained refugees in Nairobi," Human Rights Watch says in a statement.
"To our knowledge, no refugee was charged with criminal acts or terrorist-related activities."
Children held
After one raid on 29 November, 54 Sudanese and Congolese refugees spent the night in "deplorable" conditions at Muthangari police station in Nairobi, the report said, quoting an official from the UN refugee agency UNHCR.
The UNHCR was not allowed access to the refugees until midday on 30 November, when the refugees with documents were released, Human Rights Watch says.
But some of the Sudanese refugees remain in detention.
A UNHCR official quoted in the statement said a Congolese refugee woman was held along with her child and she counted about eight other children who were detained along with their mothers.
"The recent round of arrests is just the latest example where the Kenyan police have committed rights violations against refugees," Human Rights Watch says.
"Acts of violence, however terrible, never justify a government round-up of refugees. Kenya will not help improve its international image by scapegoating marginal groups such as refugees."
Mombasa probe
The organisation says refugees in Kenya are at risk not only because of potential violence from criminals but also because of Kenyan police "who should be protecting refugees, not abusing them".
Fourteen people have been arrested in connection with the Mombasa attacks, which US President George Bush has blamed on Osama Bin Laden's al-Qaeda network.
In Nairobi, the British High Commission in Kenya evacuated its staff from its building in Nairobi after a threat was received.
Spokesman Mark Norton would not elaborate on the nature of the threat but he said it was specific and was being treated seriously.