"This person was on Ukrainian territory illegally and therefore, in compliance with all legal procedures, he was returned to the country from where he arrived," spokesman Oleh Slobodyan said in a post on Facebook.
Earlier, Saakashvili’s spokeswoman said he was detained in Kiev by unidentified people in camouflage, adding that the intention might be to deport him from Ukraine.
It was not immediately clear who was responsible for the detention, but last week Saakashvili's lawyer said he could face imminent deportation or extradition after he lost a court appeal.
A video posted on Saakashvili's official Facebook page showed several men in green military uniform approaching a man lying on the floor of a restaurant.
"Unknown people in masks seized Mikheil Saakashvili and took him away ... The kidnappers were in three white minivans," a Facebook post on the same page read.
His spokeswoman said the border service was likely behind the move.
"We regard this as a detention with the aim of then deporting Saakashvili from the country. They could illegally send him to Poland," she said by telephone.
The Ukrainian border service declined to comment when asked about the detention, but said they might have information at a later stage.
Kiev police were not involved, the police spokeswoman said.
The former president of Georgia entered Ukraine last September despite being stripped of his Ukrainian citizenship in a protracted standoff with the Kiev authorities, whom he accuses of corruption.
Saakashvili was granted Ukrainian citizenship and invited by President Petro Poroshenko to become governor of the Odessa region after the "Maidan" protests ousted a pro-Russian president in early 2014, but the two later fell out.
There was no immediate sign of public outcry against the latest detention, unlike the street protests that allowed Saakashvili to escape police custody in December - one of the more dramatic twists in his long-running cat-and-mouse game with the Ukrainian authorities.