Sheikh Ali al-Qaradaghi said the union will file a complaint against those responsible for the attack.
He also dismissed claims that the IUMS interferes in the internal affairs of Tunisia, Al Jazeera reported.
The head of the Tunisian Free Constitutional Party, Abir Moussi, on Tuesday escorted party members in breaking into the branch in Tunis.
The Tunisian branch of the IUMS also slammed the move.
“Such an act was a serious threat to the safety of the union’s members who were present,” said Lutfi al-Amdouni of the union’s board of directors.
Al-Amdouni said the government and Interior Ministry did not respond to the action and he accused Moussi of terrorism and described it as “scandalous for the Tunisian state”.
He said the union’s branch in Tunisia is licensed and has agreements with the Tunisian Education Ministry and holds activities, seminars and conferences with the participation of scholars and intellectuals from different countries.
Moussi, whose party has 16 lawmakers in the 217-seat Tunisian parliament, said on several occasions that she is against the Tunisian revolution in 2011 which brought down long-time ruler Zine El-Abidine Ben Ali.
The Union's headquarters is based in Doha, Qatar but it has several branches in several Arab and Islamic countries where it conducts activities that encourage peaceful coexistence, reject extremism and introduce Islam within its message of tolerance and moderation.