At least seven people have been killed and dozens injured since ethnic unrest began in the impoverished southeast of Nepal nearly two weeks ago.
Thapa was the home minister in April last year, when King Gyanendra was forced to end a 14-month period of absolute control in Nepal following mass protests organised by political parties and rebel Maoists.
Since the king’s climbdown, a high-level commission charged with investigating abuses of authority during royal rule has recommended that action be taken against Thapa.
A Nepali minister from the ethnic Madhesi community has meanwhile resigned, accusing the ruling alliance of neglecting Madhesi grievances that have led to violent protests in the south.
Madhesi activists say their community has been discriminated against by “hill-dominated” political elites who run the country, resulting in its under-representation in government, security agencies and the highest levels of politics.
The resignation by Hridayesh Tripathi, the country’s commerce minister, is the first by a senior Madhesi politician and comes amid rising criticism that the government has not called protest leaders for talks.