The men, who had been studying at a religious school in Pakistan, were trying to catch a flight on Monday night when they were intercepted.
"We have no evidence that there are any links at all between the students and any criminal organisation, so news that there is a link between ISIS and the students is not true," said Sansern Kaewkamnerd, a deputy government spokesman.
In a statement on Saturday, Thailand's Foreign Ministry said the five Thais were still being held in Pakistan, contrary to earlier reports that one was being held and four had been freed.
Thai national security chief Anusit Kunakorn said on Friday that four of the group were being sent back to Thailand.
On Friday, Thai newspaper the Bangkok Post reported that two of the five were suspected of having links to Islamic State, which is also known as ISIS. The report cited intelligence sources.
An investigation into the students' families found no links with violence in Thailand's southern region, where there has been a long-running Muslim separatist insurgency, Army Chief Udomdej Sitabutr told reporters on Friday.- Reuters
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