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Pakistan's navy has pulled out of anti-piracy operations in the western Indian Ocean, following disagreements with the US, Al Jazeera reported on Wednesday.

Naval ships will no longer operate with the counterpiracy Combined Task Force (CTF) due to a decision by the US to cut fuel subsidies for Pakistani patrol boats, sources told the broadcaster.

The force was set up to quell an outbreak of piracy off the coast of Somalia and beyond, particularly in the western Indian Ocean region.

Shipping in the area now operates relatively unheeded thanks to the multinational task force.

Pakistan played a lead role in the naval armada, and headed the task force on several occasions.

The CMF said other nations that are part of the task force will fill the gap caused by Pakistan's withdrawal.

"Currently, Pakistan provides experienced naval personnel, very knowledgeable in areas such as operating in the Indian Ocean," CMF spokesperson Wendy Wheatley told the broadcaster.

"The current constituents of CTF 151 does not include Pakistan, however, a new team of nations take over every 4-6 months... Participation remains purely voluntary and no nation is asked to carry out any duty that it is unwilling to conduct."

Pakistan will continue to operate in the Combined Maritime Forces that operates in the Indian Ocean and Red Sea.

US-Pakistan relations have hit a new low under President Donald Trump, who cut training for Pakistan officers and $300 million in military aid.

Fraught ties between the two countries have centered on the US' so-called "war on terror", with Pakistan's military and intelligence community accused of having ties with the Afghan Taliban.

Islamabad also has historically close ties with China, and warming relations with Iran, particularly under Pakistan's new Prime Minister Imran Khan.