Undercover soldiers dressed in Arab clothing and using a vehicle with Palestinian number plates pulled over three Palestinians travelling on the outskirts of the northern city of Jenin, witnesses said.
Shots were heard during Thursday's incident but there were no reports of casualties.
Targeting Islamic Jihad
An Israeli military source said three suspected members of Islamic Jihad were arrested in Jenin.
Islamic Jihad said the three detainees were armed leaders in the movement and warned that a de facto Palestinian truce, in place since January, would not hold if Israel continued to wage a full-scale operation against the group.
"We are surprised that the Palestinian Authority have remained silent over what's happening against us"
Islamic Jihad statement
Soldiers also arrested another three Islamic Jihad members overnight outside the West Bank city of Ram Allah, said the army and the group.
Islamic Jihad said two of the three were students at the West Bank's prestigious Beir Zeit University.
Breaking the truce
"The truce will not have a future if Israel continues their operations against us," the faction said in a statement.
Israel agreed earlier this year to suspend arrest operations but says it retains the right to detain suspects who are thought to pose an immediate security threat.
"We are surprised that the Palestinian Authority and Palestinian parties have remained silent over what's happening against us. There must be a reaction against this operation," the movement said.
Meanwhile, the Palestinian Bar Association has called on the Palestinian authority to put an end to the chaos in the territories, reported Aljazeera.
Quraya under pressure to control
security in Palestinian areas
In a memorandum to Palestinian Prime Minister Ahmad Quraya, the association called for arresting the perpetrators of violence against judges, attorney-general's staff and lawyers.
Dozens of lawyers supported by Palestinian citizens on Thursday took to the streets in Ram Allah to publicise their demands.
Aljazeera correspondent Walid al-Omari said the protests were response to the chaos and security breakdown threatening the courts, judges and others in the judiciary.
Most of the judiciary staff have been threatened or beaten by armed men or tribal groups.
The last few days have witnessed a serious deterioration in security with armed men opening fire at homes of Palestinian officials and attacks in the hearts of Palestinian towns, al-Omari said.
Some Palestinian lawyers have even claimed they were no longer able to stand in court and defend their clients.