Deputy Interior Minister Thaworn said he was, Thaksin's lawyer confirmed it, and Thaksin himself did in his interview with a radio station in Udon..... but the Malaysians deny he was there as The Star reports:
Former Thai premier Thaksin Shinawatra, who is now a fugitive, was never in Malaysia nor was he given any protection by the Special Branch as he has claimed, Inspector-General of Police Tan Sri Musa Hassan said.
Musa said Malaysian police had no knowledge of any visit by Thaksin, despite earlier reports quoting Deputy Interior Minister Thaworn Senneam as saying Thaksin had been spotted in Malaysia recently, but left the country before he could be arrested by the authorities.
Thaworn said Thai embassy officials had informed the Malaysian authorities to seek Thaksin’s arrest and extradition.
“We were only alerted by the Thai embassy here of the fugitive’s supposed presence early this month following a news report in Bangkok.
“As far as we are concerned, he was never in the country and we did not send 20 Special Branch officers to protect him. We have checked with local hotels, Immigration and other sources, and there is no evidence to show that he was ever here,’’ he said.
BP: That reference to the 20 Special Branch officers was in relation to what Thaksin said in the radio interview (actually he said 15 as per a transcript of the interview and not 20 as The Nation reported), but neither Thaworn or Thaksin came looking good given the Malaysian denial. So will Thaksin provide evidence that he was in Malaysia? The Malaysian answer "[a]s far as we are concerned" has the ring non-denial denial.

My personal thought is he was in Malaysia and the Malaysians did give him an escort of some kind, but now all evidence has been dealt with. Malaysia is not about to come out to admit it knowing it would cause a regional conflict days before the summit and knowing the current government's willingness to flex it's military muscle in the northeast with Cambodia.
Malaysia could well just be sitting as a spectator wondering who will come out on top of the Thai power struggle before it actually makes a commitment on which way it is leaning.
If Thaksin, or his supporters, did get back in to power the last thing Malaysia would want is their neighbor to have vindictive feelings toward them.
Whether he was there or not is irrelevent. The story just gets him publicity in Thailand and the more it is discussed the more publicity. Tjhis kind of medai play is classic Thaksin and is done repeatedly and his opponetns always fall for it.
Avudh had a piece about Thaksin's media plays the other day.
Off topic a bit, Thaksin's obsession with being a big man and being welcomed by big people is a little disturbing imho.