Reports of a meeting with Wong Kan Seng, Singapore’s other deputy prime minister, have not been confirmed.
Surayud Chulanont, Thailand’s caretaker prime minister, said on Tuesday: "We informed the Singaporean [ambassador] that we are concerned by the political movements made by Thaksin.
"Singapore should be more cautious about allowing such movements since we have already revoked Thaksin's diplomatic passport."
Kitti Wasinondh, a foreign ministry spokesman, said: "The Royal Thai government was dissatisfied with the incident and the explanation."
Singapore's foreign ministry said Chan had "explained that the Singapore government regarded this as a private visit''.
In a statement issued on Sunday, it had described Jayakumar as an "old friend'' of Thaksin's and said their meeting was "purely social and private".
Since being unseated, Thaksin has made high-profile trips to China, Hong Kong and Indonesia.
The Thai government has said that he was behind the New Year's Eve bombs in Bangkok that killed three people with the intention of undermining confidence in the government.
But Thaksin, who said last week that he was giving up politics, denies he is trying to make a political comeback.
On Monday night, Thaksin appeared on CNN but the interview was blacked out by Thailand's satellite channel operator, UBC.
Colleagues in court
Meanwhile on Tuesday, members of Thaksin's former Thai Rak Thai party were in court to fight allegations of electoral fraud.
The party is accused of bankrolling token opponents to stand in last year's April election, after their main opposition - the Democrats - boycotted and in effect nullified the results.
Hundreds of Thai Rak Thai MPs, including Thaksin, have resigned from the party, hoping to escape penalties, including being banned from political activity for up to five years.
But critics are sceptical about the motives and legitimacy of the tribunal set up after the coup.
They say the military has torn up the country's constitution, and there is a growing disillusionment over the coup leaders' promise of elections in October and worry that the military wants to hold on to power.
On the economic front, retailers and restaurant owners say business is slow and investors are smarting from new foreign ownership restrictions.
Thaksin said the post-coup administration, which introduced capital controls in December to stem a rise in the baht and then tightened up foreign investment laws, was taking the country down the road to economic isolation.