Malaysian police said the refugees, who included women and children, were trying to escape violence in Thailand's troubled southern provinces, where almost 900 people have been killed since January of last year.
But Thaksin said that Islamic militants were among the group and were trying to attract international attention to their cause, Channel NewsAsia reported Friday.
Malaysia's Foreign Minister Syed Hamid Albar said Thursday that his country would provide temporary shelter to the Thai refugees, who have no travel documents, but would not grant them asylum.
Thaksin described a recent wave of bomb blasts in the southern provinces as retaliation after the government issued arrest warrants for suspected insurgents. Some 20 blasts have killed one police officer and injured 21 other people.
The prime minister also called on mobile phone operators to introduce new technology within two months to prevent bombs from being detonated by mobile phones.