Ali Larayedh, who served as premier from 2013 to 2014, was detained as part of an investigation into alleged participation of the departure of thousands of young Tunisians to fight with jihadist groups abroad.
As many as 6,000 Tunisians travelled to Libya, Iraq and Syria to volunteer as foreign fighters, a number that secular opposition groups say indicates deliberate neglect.
The investigation, which has also targeted Ennahdha's veteran leader Rached Ghannouchi, was launched after the vehemently anti-Islamist president sacked the government and suspended parliament in July 2021.
The arrest of the Ennahdha number two comes just days after nearly 90 percent of voters boycotted an election to a toothless new parliament established by Saied following his seizure of sweeping powers in 2021.
Saied has defended his power grab as necessary to end the repeated political crises that accompanied the North African country's transition to democracy following the first of the Arab Spring revolutions of 2011.
But his efforts to legitimise his new powers have been repeatedly snubbed by voters, first in a widely boycotted July referendum and then in Saturday's parliamentary election.
Ennahdha, which like almost all Tunisian parties boycotted the vote, accused Saied's government of "systematically targeting" its leadership.
The party said that Larayedh's arrest marked a "desperate effort by the coup administration and its president, Kais Saied, to cover up the farce of the parliamentary election which was boycotted by 90 percent of voters".
Ahmed Nejib Chebbi, president of the country's main oppostion coalition, told journalists on Tuesday that the arrest was intended "to distract attention from the results of an election ignored by the public".
Chebbi's National Salvation Front, which includes Ennahdha, had said the slim election turnout should be a cue for Saied to step down.
But Saied hit back at his critics Monday, noting that some of them had criminal charges hanging over them, a veiled reference to investigations into Ennahdha officials.