The Ministry of Foreign Affairs condemned the "unilateral action" in Orakzai Agency, carried out by the RSM which targeted an Afghan refugee camp saying this was "detrimental to the spirit of cooperation between the two countries in the fight against terrorism".
Pakistan considers US drone strikes a violation of its sovereignty, while the USA accuses Pakistan of providing safe havens for militants, a charge Pakistan denied saying it acts against militants without discrimination.
The US Embassy in Pakistan on Thursday dismissed a claim by Islamabad that US forces bombed a refugee camp on its territory.
In the first U.S. drone strike of the year on January 17, a man was injured in Kurram tribal region.
"Out of total 54 Afghan Refugees Camps/complexes in Pakistan, 43 are in KP with overlap in FATA", said a press release shared by the ISPR.
This is the second drone attack in Pakistan's tribal areas this year.
Almost 1.4 million Afghan refugees remain in Pakistan, according to UNHCR figures.
"Their presence in Pakistan helps Afghan terrorists melt and morph among them", it said. "This is the reason we feel repatriation of Afghan refugees is essential". The strike occurred in the Mata Sangar area of Kurram.
Another source said the house was destroyed in the attack and two militants, identified as commander Ihsanullah alias Khuraye and his associate Nasir Mehmood, were the target. A source close to the Haqqani group confirmed that at least one mid-level Afghan commander had been killed.
Already frosty relations between the US and Pakistan - the two allies in so-called war against terrorism - have further nosedived since President Donald Trump assumed the office in January previous year, mainly due to a clash of interests in war-ravaged Afghanistan.
Two missiles were shot at a house in Speen Thal Dapa Mamozai area, according to the political administration.