The crackdown, which has seen people held in police cells or a football stadium, follows a spate of attacks in Kenya by suspected supporters of Somalia's Al-Qaeda-linked Shebab rebels.
A batch sent to Somalia by airplane on Tuesday was the fourth round sent home, taking the total expelled to 359, HRW said.
"Deporting people to conflict zones in Somalia shows a total disregard for their rights and their safety," said HRW's Gerry Simpson, adding that returning refugees against their will to a war zone is unlawful.
The UN's refugee agency has said it was "concerned" at the wave of arrests and has demanded access to those detained.
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The Shebab yesterday vowed to move their war to Kenya, in a broadcast by a top commander urging fighters to rise up against Nairobi.
Kenyan troops crossed into southern Somalia in 2011 to fight the Shebab, later joining the now 22,000-strong UN-mandated African Union force battling the Islamists.
Fighter jets, believed to be from Kenya, pounded Shebab strongholds this week, as part of the latest push against the insurgents by the AU force, which said it was targeting its "senior leadership and foreign fighters" and boasted of having killed over 50 rebels.
Yesterday a grenade blast in the port city of Mombasa wounded two police officers.
Kenya's key tourism industry has been badly damaged after western nations issued warnings advising travellers to avoid Mombasa due to the threat of attacks.
Last week two British tour operators evacuated hundreds of tourists from coastal resorts.