He also suggested Russia was behind the mutiny, saying those involved had "connections with special forces in a specific country known to us".
"I am asking and demanding from our northern neighbour to refrain from provocations," he said.
But Moscow's envoy to Nato denied any involvement in the mutiny, saying Saakashvili was attempting to distract attention from domestic problems within Georgia.
"The fact that a mutiny broke out at a Georgian defence ministry brigade is just a reflection of the all-embracing political and economic crisis that is developing under Mikheil Saakashvili's presidency," Dmitry Rogozin told the Reuters news agency.
"Saakashvili and his entourage are trying to explain the consequences of their foolishness by [accusations of] Moscow's underhand plotting."
Earlier an interior ministry spokesman said they had uncovered a Russian-backed plot to overthrow the government, organised by a former special forces commander.
Shota Utiashvili, Georgia's interior ministry spokesman, said the "rebels were in direct contact with Russians" and were receiving orders and money from them.
He said the organisers of the plot were former high-ranking defence ministry officials, and that at least one had been arrested.
Matthew Collin, Al Jazeera's correspondent in Tbilisi, said Saakashvili was heading into the military base, signalling that the rebellion could shortly be over.
He said it was unclear how serious the mutiny was, but it was "clearly bad news for Mikheil Saakashvili, the country's president, who has been facing demonstrations in the capital over the last few weeks demanding his resignation.
He said it was not clear whether the rebellion would affect the upcoming Nato exercises, which will be taking place at a "very different military base".
"There is nothing to suggest the mutiny has spread beyond this base or that it will place the exercise under threat," he said.
Sikharulidze said the government was in negotiation with the soldiers at the base.
"The rebellion continues. Law enforcement agents are on the scene," he said.