Lawmakers from the Cambodia National Rescue Party (CNRP) pulled out of parliamentary sessions in May after some MPs, including its deputy leader Kem Sokha, were slapped with legal cases by the government.
With 2018 elections in view, Hun Sen is increasingly using Cambodia's pliant courts -- as well as his political cunning -- to box in rivals, a tactic he has deployed throughout his 31-year tenure in office.
On Tuesday 39 opposition MPs ended their boycott and joined the parliamentary debate on a $5 billion budget for 2017.
He dened his party had caved in to Hun Sen's pressure tactics but said his party "are the victims of political crackdown."
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"This (end of boycott) is also a gesture to show that we want a resolution" to the political crisis, he said.
Ruling party officials could not immediately be reached for comment.
The opposition are increasingly cramped in the run-up to elections.
Their leader, Sam Rainsy, is in self-exile in France to avoid arrest on charges which he says are politically motivated.
His deputy Kem Sokha has since May been holed up inside party headquarters in Phnom Penh.
Last week an opposition senator was handed a 18-month jail sentence over a defamation case filed by Hun Sen.