Palestinian Prime Minister Ismail Haniya has criticised a decision by President Mahmoud Abbas to assume control of Gaza's border crossings.
Abbas has appointed an ally to head internal security
He called the move an attempt to undermine the Hamas-led government's control over security matters.
The government would not accept the creation of parallel structures that would diminish its authority, he added.
Mr Abbas, whose Fatah party is a political rival of Hamas, also named an ally as head of internal security.
In his new role, Rashid Abu Shbak, who is currently head of the Fatah-dominated Palestinian Preventative Security Service, will have authority over the police and emergency services.
Correspondents say that although Mr Shbak will nominally report to Hamas Interior Minister Said al-Siyam, ultimate authority rests with the president.
Mr Abbas issued a presidential decree on Wednesday, taking over control of the Palestinian border points and crossings.
But on Thursday, Mr Haniya said he rejected any attempts to take power away from Hamas.
He told the Associated Press news agency Mr Abbas had assured him the security forces would remain under the control of the Hamas-led cabinet, which he said had not taken power "on the back of a tank", but in "transparent and fair elections".
Despite the victory of the militant group in January's parliamentary election, Mr Abbas retains wide-ranging powers.
He is head of the National Security Council, which has final say over the Palestinian security forces.
Hamas took formal control of the government last week, after being sworn in by Mr Abbas.
The BBC's Alan Johnston in Gaza says the new Palestinian government has a severe lack of experience. None of its ministers have been in government before and they have taken over ministries packed with officials loyal to the Fatah party.
Mr Abbas and Mr Haniya are due to meet in Gaza on Friday evening.