The news emerged as Palestinian president Mahmud Abbas said Israel had informed him it would cut all ties with his incoming interim government, which is to be sworn in at his West Bank headquarters on Monday.
And he also warned in remarks late on Saturday that the Palestinians would respond to every punitive step taken by Israel in respect to the new government.
The three ministers elect had applied to cross from Gaza to the West Bank on Thursday, but their application was immediately rejected, a senior Palestinian official responsible for coordinating exits and entries told AFP.
"We sent the application in on Thursday and explained that these officials are to be sworn in as ministers in Ramallah, but Israel immediately rejected the application," he told AFP on condition of anonymity.
COGAT, the Israeli defence ministry unit responsible for Palestinian civilian coordination, refused to comment on the matter, as did the office of Prime Minister Benjamin Netanyahu.
Earlier, public radio said COGAT head Major General Yoav Mordechai had vetoed the request, without saying why.
On April 23, rival Palestinian leaders in the West Bank and the Hamas-run Gaza Strip announced a surprise unity deal, pledging to work together to set up an interim government of political independents.
But Israel immediately called a halt to crisis-hit peace talks, vowing it would never talk to any government backed by Hamas, whose charter calls for the destruction of the Jewish state.
And with the promised government to be sworn in at a ceremony on Monday, Israel appeared to be making good on its threat.
Speaking late on Saturday, Abbas said Israel was looking to punish the Palestinians for overcoming their years-long internal political differences.
"Israel wants to punish us for agreeing with Hamas on this government," he said, explaining that Israeli officials had informed him that the Netanyahu administration would "boycott the government the moment it is announced".
But the Palestinians would have an answer for every Israeli move, he warned.
"Each Israeli step will have a proper Palestinian response," he warned, without elaborating.
"We will take everything step-by-step, we will not be the ones to react first."
He appeared to be alluding to Palestinian intentions to seek further recognition for their promised state in the international diplomatic arena.
Such moves were put on hold for nearly all of the nine-month US-led peace talks, which collapsed in late April, but resumed after Israel blocked the promised release of two-dozen veteran Palestinian prisoners.
The new government, which will pave the way for long-overdue legislative and presidential elections, will be chaired by Rami Hamdallah, who is currently serving as prime minister in the Fatah-dominated West Bank administration.