"The mechanisms of governing Bosnia cannot be held by the international community while I'm supposed to be taking over responsibilities," he said, adding that his decision was "neither a whim nor a provocation".
Bosnia's presidency is expected to review Spiric's resignation at an extraordinary session on Friday.
The political crisis is the most serious in Bosnia since the end of its bloody inter-ethnic 1992-1995 war, which was settled by the Dayton peace accords.
The accords split Bosnia into separate Serb and Muslim-Croat entities with a weak central government with three ministers from each ethnic group.
"Twelve years after Dayton, foreigners have exclusive rule over this country"
Nikola Spiric, Bosnian PM
The reform proposals are backed by the international Peace Implementation Council comprising more than 40 countries and international organisations that oversee the conditions of the peace agreement.
Last month Miroslav Lajcak, the international community's High Representative to Bosnia introduced the EU-backed reforms aimed at improving the efficiency of Bosnia-Herzegovina's central government.
The proposals would change the way a quorum is calculated in order to make it more difficult for legislators to block decisions simply by not showing up.
The Bosnian parliament has until December 1 to adopt the measures designed to streamline the state's decision-making process, said Lajcak, or he will impose them.
Commenting on the prevailing situation, Spiric said Bosnia-Herzegovina "is unfortunately not a sovereign state" 12 years after the peace deal.
"Twelve years after Dayton, foreigners have exclusive rule over this country and I believe this isn't good for this country or its citizens," he added.
The move has outraged other Serb leaders who said the changes will diminish their federal role and increase Muslim domination.
They have also threatened to resign en masse if the reforms were not withdrawn.
In a statement, Lajcak said Spiric's decision "is not a responsible action" and "will not calm the current political situation".
He said the new measures would not undermine Bosnia's three ethnic groups – Muslims, Serbs and Croats – and called on the government to respect its legal duty to perform in its full capacity until the situation is resolved.
Lajcak said it was "paradoxical" for Spiric to resign over changes designed to make his work easier.
The EU has made reforms a main condition for Bosnia's bid to join the 27-member bloc, and one of the key measures is to unite its police forces.