"Nobody in the international community should interfere until we resolve this issue ourselves," he added.
He said the Macedonians were being pushed too far, especially over a possible constitutional change giving equal status to the Albanians who make up some 30% of the population.
He also said he was leaving the Co-ordination Body for Crisis Management because the main ethnic Albanian parties on it favoured bringing in an outside mediator.
The Macedonian interior minister added that the Macedonian security forces were able to sort out the problem without international interference.
"I support an energetic resolution of the crisis. I stand for peace, but for peace which shall be brought by the Macedonian security forces because we have enough potential and energy to do so," he said.
"Nobody in the international community should interfere until we resolve this issue ourselves," he added.
A BBC correspondent says the minister is a known hard-liner and his resignation is the first highly visible crack in the negotiations.
Mr Boskovski's announcement came on the fifth day of talks aimed at finalising details of a peace plan.
The American State Department said earlier that there had been progress in the talks, which have been going on for nearly a week.
US State Department spokesman, Richard Boucher, said: "Political leaders representing both the ethnic Macedonians and ethnic Albanians have put on the table very serious concrete proposals.
"This demonstrates that there is a process, that it is moving constructively forward and we encourage them to achieve results on a variety of political reforms," he added.
But US President George W Bush urged the quick completion of the peace plan.
"We strongly support that process," he said.
Trajkovski plan
The cross-party body was set up as part of President Boris Trajkovski's package of proposals to restore peace in the country and is charged with overseeing military aspects of the peace plan.
The Trajkovski plan, backed by Nato and the European Union, allows for a partial amnesty for Macedonian-born guerrillas and their disarmament by Nato troops.
The rebels are demanding wide-range concessions, including a constitutional change to name them as an equal community with the Slav majority.
On Monday, Macedonian forces and rebels exchanged mortar and artillery fire.
The clashes were described as the most serious since the government's decision to temporarily halt to its military operations against the National Liberation Army (NLA).