Israel has accused six prominent Palestinian human rights groups of being terrorist organisations, saying they have undercover links to a militant movement.

Most of the groups document alleged human rights violations by Israel and the Palestinian Authority.

The six are Al-Haq, a human rights group founded in 1979, Addameer, Defence for Children International – Palestine, the Bisan Center for Research and Development, the Union of Palestinian Women’s Committees and the Union of Agricultural Work Committees.

The Israeli defence ministry said they were linked to the Popular Front for the Liberation of Palestine (PFLP), a secular political movement with an armed wing that in the past carried out attacks against Israel.

The groups “were active under the cover of civil society organisations, but in practice belong and constitute an arm of the [PFLP] leadership, the main activity of which is the liberation of Palestine and destruction of Israel”, the defence ministry said.

It claimed they were “controlled by senior leaders” of the PFLP and employed its members, including some who had “participated in terror activity”.

The groups serve as a “central source” of financing for the PFLP and had received “large sums of money from European countries and international organisations”, the defence ministry said.

The groups, well known for their human rights work, have received funding from EU member states, the United Nations and other donors.

The Palestinian Authority said the move was an “unhinged assault” on Palestinian civil society.

“This fallacious and libelous slander is a strategic assault on Palestinian civil society and the Palestinian people’s fundamental right to oppose Israel’s illegal occupation and expose its continuing crimes,” it said in a statement.

Shawan Jabarin, the director of Al-Haq, said the move was an attempt to stifle criticism. “They may be able to close us down. They can seize our funding. They can arrest us. But they cannot stop our firm and unshakeable belief that this occupation must be held accountable for its crimes,” he told the Times of Israel.

The Israeli human rights group B’Tselem called the government’s declaration “an act characteristic of totalitarian regimes, with the clear purpose of shutting down these organisations”.

It added: “B’Tselem stands in solidarity with our Palestinian colleagues, is proud of our joint work over the years and is steadfast to continue so.”

The Israeli government has previously cracked down on Israeli, Palestinian and international human rights organisations by clamping down on funding, denying entry to employees, and raiding offices.

The PFLP is designated a terrorist organisation by Israel, the US and the EU.