UGTT chief Noureddine Taboubi says "The message is clear that the UGTT is being targeted."
"The president is trying to divert attention from what happened in the second round of legislative elections and the utter failure of his economic and social decisions," Taboubi added.
"The state is using intimidation to repress the opposition," he said.
On Sunday the North African country completed an election to a parliament Saied stripped of its powers last year, a vote boycotted by almost 90 percent of the electorate.
Saied has been accused of using the judiciary to silence his political opponents since he launched a dramatic power grab in July 2021 in the birthplace of the pro-democracy Arab Spring uprisings.
The UGTT chief's slam at President Saied came following the arrest of the union's senior official Anis Kaabi earlier this week..
The head of the million-member union federation, which jointly won the 2015 Nobel Peace Prize for its role in Tunisia's democratic transition, said Kaabi had been arrested to send "a clear message, that the UGTT is a target."
Kaabi was detained on Monday after workers at toll barriers on Tunisian highways went on strike for better pay, meaning tolls usually paid to the state-owned highways company went uncollected for two days.
Tunisie Autoroutes had made two formal complaints against him for financial losses stemming from the strike, local media reported.
Hours before Kaabi was detained, Saied had threatened "those who block roads", saying that they "cannot remain unaccountable".
The UGTT said the arrest was a "violation of union rights as well as international treaties" signed by Tunisia.
On Thursday, Kaabi was placed in pre-trial detention ahead of a February 23 court hearing on charges of "exploitation of his status as a civil servant with a view to prejudicing the administration", media reported.
Saied's rivals have accused him of seeking to reinstall a dictatorship in Tunisia.
Many observers saw Sunday's 11.4 percent turnout as a rejection of Saied's overhaul of the country's post-revolution political system, which has given his office far-reaching powers and made him as good as unimpeachable.
Tunisia is also going through a severe economic crisis with 10 percent inflation and repeated shortages of basic goods.