Mokhtar Trifi, the league's president, said: "The decision is not a surprise – it is a political decision dressed up as a judicial one."
The activists who lodged the complaint are also members of Tunisia's leading ruling party, the Constitutional Democratic Rally.
Trifi said: "What is surprising is the timing, as we were expecting a period of greater openness towards rights groups in Tunisia."
The league's leadership says the excluded members are government stooges who want to undermine the independence and credibility of the league, founded in 1977.
"The court's decision has protected us from the offences of the league, which wants to remove opponents seen as pro-government"
Chedli Ben Younes, excluded league member
They in turn accuse the league's leadership of cronyism, physical and verbal violence and sidelining members who disagree with them.
Chedli Ben Younes, a lawyer and one of the excluded members, said the leadership had acted illegally.
"The court's decision has protected us from the offences of the league, which wants to remove opponents seen as pro-government."
The government says it has not intruded in the dispute and insists it is committed to democracy and respect of human rights.
When the group attempted to meet in Tunis last May, dozens of police officers blocked their path.
Witnesses said that activists who tried to breach the cordon were kicked and beaten.