Prime Minister Ranil Wickremesinghe informed his cabinet of the decision to replace the three heads of the Commission to Investigate Allegations of Bribery or Corruption (CIABOC) after the August 17 general election, a government spokesman said.
"Investigations have been delayed by at least six months because of the obstructionist attitude of the commissioners," spokesman Rajitha Senaratne told reporters.
"Two of them also face allegations (themselves) of corruption," he said without elaborating.
But the panel has blocked recruitment of 50 new officers to investigate a backlog of complaints, and prevented the hiring of forensic auditors to help with ongoing investigations, Senaratne said.
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He said the three also refused to release four CIABOC officers for specialised training offered by the US government which is helping Sri Lanka trace the billions said to have been stolen.
Under Sri Lankan law, the three CIABOC commissioners must give their approval before detectives file legal action against suspects and must also agree to any new investigations.
Rajapaksa lost the January presidential election partly on allegations of corruption and nepotism. But the former president is staging a political comeback by contesting a seat at next month's parliamentary poll.