Baroness Ashton, the EU's foreign policy chief, yesterday issued an unusually sharp rebuke to Israel over a military court's conviction of a Palestinian activist prominent in unarmed protests against the West Bank separation barrier.

Lady Ashton said she was "deeply concerned" that Abdallah Abu Rahma was facing a possible jail sentence "to prevent him and other Palestinians from exercising their legitimate right to protest against the separation barriers in a non-violent manner".

Though acquitted on two charges - including one of stone-throwing - Mr Abu Rahma, 39, a leader of the anti-barrier protests which have taken place every Friday for five years in the West Bank village of Bil'in, was convicted on Monday on another two: "incitement" and "organising and participating in an illegal demonstration".

He is in jail, awaiting sentencing next month. He was detained last December by troops who arrived at his Ramallah home at 2am in seven jeeps as part of what anti-barrier activists say has been an escalating wave of arrests of protesters in West Bank villages, angry about the barrier and settlements encroaching on Palestinian land.

Pointing out that the European Union regarded the barrier as "illegal" where - as at Bil'in - it was built on Palestinian land, the EU's High Representative for Foreign and Security Policy said the EU considered Mr Abu Rahma, who works as a teacher at a private school, to be "a human rights defender committed to non-violent protest".

The protest by Lady Ashton, who was yesterday accused by Israel's foreign ministry of "interfering" in the country's judicial process, follows mounting concern by Western diplomats over the severity of measures taken by Israeli security forces against the mainly rural protests. Officials from several European countries, including Britain, were present for the verdict in the Ofer military court on Monday.

Her intervention was partly designed to demonstrate that the EU representatives will continue closely to watch developments on the ground in the West Bank while direct peace negotiations, due to start in Washington next week, get under way.

The military judge also acquitted Mr Abu Rahma of a charge of illegal arms possession which arose from a collection of used tear gas canisters and bullet cases he had been making to demonstrate that police and troops used violence against protesters.

The Popular Struggle Co-Ordination Committee said the "absurd" charge demonstrated the lengths the military was prepared to go to "to silence and smear unarmed dissent".

It added that the incitement charge had been upheld even though it was based on the testimonies of minors who had been arrested in the middle of the night, and which the court recognised had defects. No other evidence had been offered, despite the routine filming of the protests by the security forces. It said the charge of organising demonstrations had not been used since the first intifada, from 1987 to 1993.

In 2008 Mr Abu Rahma was given an award by the International League for Human Rights in Berlin for "outstanding service in the realisation of basic human rights". He met "the Elders", a group of global statesmen and women including Archbishop Desmond Tutu, when they made a solidarity visit to Bil'in last year.

The protests at Bil'in, the highest profile of several in West Bank villages, have seen clashes between security forces using tear gas and rubber bullets and stone-throwing youths. After a protester was killed there in April 2009, military prosecutors said there was insufficient evidence for an investigation.

Construction work on rerouting part of the barrier at Bil'in finally began this year after the state had twice been found in contempt by the Supreme Court for failing to implement a 2007 court order to reroute the barrier.

Yigal Palmor, Israel's Foreign Ministry spokesman, said: "In a country in which even open supporters of Hamas and Hizbollah enjoy freedom of speech, Lady Ashton's accusations sound particularly hollow. If she thinks she can do a better job than the defendant's lawyer, she should say so. Otherwise, interfering in a transparent legal process in a democratic country is a very peculiar way to promote European values."

But Mr Abu Rahma's lawyer, Gaby Lasky, said: "The international community must take a tough stand on this issue, and I am happy that the political motivation of the indictment against a human rights defender was clear to the EU from attending the hearings."

The Co-ordination Committee, a loose body of protest organisers, said yesterday there had been a "dramatic" increase in arrests. Of 93 made at Bil'in alone in five years, 46 were made since July of last year. At the more recent flashpoint of Nabi Saleh, there had been 41 arrests in the last eight months.