The two victims, aged 23 and 33, were members of the Palestinian General Intelligence Services, the ministry noted.
According to eyewitnesses, Israeli forces entered Jenin in a civilian vehicle and opened fire on personnel car.
They added that the Israelis also arrested two more Palestinians after the incident, with reports that one of them was killed. However, the ministry did not confirm the news yet.
Meanwhile, the Palestinian Presidency condemned the Israeli attack and escalation in Jenin.
Israel's attacks and violence against Palestinians are dangerously escalating the situation, the government's spokesperson Nabil Abu Rudeineh said in a statement published by WAFA news agency.
He called on the international community and the US administration to protect the Palestinian people and pressure Israel into ending its attacks.