Mike Hanna, Al Jazeera's correspondent in Colombo, said at least two arrests were made, as well as the confiscation of computers and documents.
"General Fonseka himself was not in the office ... but there does appear to be an on-going campaign of intimidation against those close to him", Hanna said.
"However, there is a feeling in Colombo that Fonseka's refusal to recognise the official election result is itself devisive. Most independent election observers say the vote ... was largely free and fair."
The government has made no official announcement on the raid, but it came a day after the government accused the opposition of planning the assassination of Mahinda Rajapakse, the newly re-elected president.
"They are trying to intimidate us as we collect evidence of vote-rigging"
Lakshman Hulugalle, the national security director, said on Thursday night that police had uncovered a "plot" to assassinate Rajapakse, who comfortably won Tuesday's election, but stopped short of saying Fonseka was directly involved.
Rauf Hakeem, an opposition spokesman, told reporters that Friday's raid was an infringement of democratic rights and an example of government intimidation.
"This is an assault on democracy," Hakeem said. "They are trying to intimidate us as we collect evidence of vote-rigging."
Security forces surrounded the hotel where Fonseka was staying as the election results were being announced on Wednesday, but he was later allowed to leave.
Fonseka has expressed fears the government would try to assassinate him.
In an interview with the BBC Sinhala-language service radio on Thursday, the former general said: "The government has informed the airport not to allow me to leave the country. I fear that an assassination attempt may be made against me."
But Al Jazeera's Mike Hanna reports that the government insists Fonseka has complete freedom of movement and could leave the country if he chose to.
He also said that speculation was rife that there will be an early parliamentary election, although the current parliament's mandate lasts until April.
"This would raise the stakes. Fonseka could again represent the opposition. He did get some four million votes and so remains a very potent political force."