The recent arrest of two respected public figures from Israel’s Palestinian Arab minority in night-time raids on their homes by the Shin Bet secret police – brought to light this week when a gag order was partially lifted – has sent shock waves through the community.

The arrests are not the first of their kind. The Shin Bet has been hounding and imprisoning politicians and intellectuals from the country’s Palestinian minority, a fifth of the population, since the birth of the Jewish state 60 years ago. Currently, two MPs from Arab political parties are facing trials, as is the leader of the popular Islamic Movement.

But the detention of Amir Makhoul and Omar Sayid is seen differently, as the gathering storm clouds in a political climate already fiercely hostile to its Palestinian citizens.

Mohammed Zeidan, the head of the Human Rights Association in Nazareth, said: “We are used to our political leaders being persecuted but now the Shin Bet is turning its sights on the leaders of Palestinian civil society in Israel, and that’s a dangerous development.” Mr Makhoul and Mr Sayid are not accused of the usual public order offences but of the much more serious charge of espionage, on behalf of Lebanon’s Hizbollah.

Mr Makhoul, who appears to be the chief object of the Shin Bet’s interest, is the head of Ittijah, an umbrella organisation co-ordinating the activities of Palestinian human rights groups in Israel. More specifically, he has become the leading voice inside Israel backing the growing international campaign for boycott, sanctions and divestment against Israel.

On Wednesday, a remand hearing in Mr Makhoul’s case was heard in court. He was not allowed to be present, and was denied the right to a lawyer until at least Monday, . He is reportedly being interrogated around the clock.

Observers from the Palestinian minority have uniformly ridiculed the allegations.

The Shin Bet’s pursuit of Mr Makhoul and Mr Sayid, according to community leaders, needs to be understood in terms of an assumption by the Israeli establishment that the Arab minority poses a political threat to the continued survival of a Jewish state.

The roots of this worldview can be traced back to the signing of the Oslo accords. With the launch of a peace process with the Palestinians, Israeli politicians began to reconsider the status of the large Palestinian minority. Many believed that allowing a significant population of Palestinians to remain inside Israel as citizens after the creation of a neighbouring Palestinian state might one day prove to be the country’s Achilles heel.

Those fears escalated dramatically when Oslo turned sour and the second intifada erupted in 2000. Israel believed the Palestinians had refused its “generous” offer at Camp David in the hope that they could use the Palestinian minority as a “Trojan horse” to destroy the Jewish state demographically from within.

Ehud Barak, the prime minister at the time, called the Arab minority the “spear point” of Yasser Arafat’s attempt to dismantle Israel as a Jewish state.

According to Mr Zeidan and other analysts, the Shin Bet’s hand in the latest arrests appears to be guided by a similar assessment that the Palestinian minority is again posing an “existential threat” to Israel – even if for different reasons.

Mr Makhoul is seen as at the figurehead of an emerging movement inside Israel that, faced with the refusal of Israelis to countenance political reforms to democratise the country, is devising new political strategies.

Israel’s military correspondents have been largely dismissive of the spying charges against Mr Makhoul and Mr Sayid. In Haaretz, Amos Harel and Avi Issacharoff pointed out that neither is privy to secrets that would interest Hizbollah.

Instead, the correspondents hinted at other motives behind the arrests. Contacts between Israel’s enemies such as Hizbollah and Palestinian rights activists in Israel are a threat, they surmise, because Palestinian leaders in Israel might offer assistance in “co-ordinating political positions” or initiate “protests and riots during sensitive periods”.

If those are in fact the substance of the Shin Bet’s charges, which remain secret, Mr Makhoul may be guilty.

He has not hidden the extensive contacts he has developed both among western Palestinian solidarity activists and in the Arab world, urging the need for a boycott of Israel. He was also at the forefront of the protests inside Israel against its attack on Gaza last year. He was called in for interrogation by the Shin Bet at the time.

“The occupation isn’t news anymore,” Mr Zeidan said. “The big threats facing Israel, in the Shin Bet’s view, are its deteriorating image in terms of human rights and the growing sense abroad that it is an apartheid state.

“Palestinian civil society in Israel, more so even than our political parties, is best placed to make the case on those issues to the international community, to expose the racism and discrimination inherent in a Jewish state. Amir Makhoul’s arrest should be understood in that light. The Shin Bet believes we have crossed a red line in our international advocacy.”

Allegations that the pair had made contact with Hizbollah, Mr Zeidan said, was an easy, “one size fits all” security charge that was difficult to challenge but persuasive to the Jewish majority. “You only need unwittingly to meet at a conference a relative of a relative of someone in Hizbollah and the Shin Bet thinks it has grounds to arrest you.”