The two countries said they agreed to charge each other with “violations” after a ceasefire following a cross-border military strike.
After Indian-managed Kashmir heard the explosion, Indian Foreign Minister Vikram Misri said that "repeated violations of the understanding we have drawn".
Soon after, the Pakistani Foreign Ministry said it was "still committed to being loyal to the ceasefire... despite violations committed by India in certain regions".
The battle between India and Pakistan has been the worst military confrontation between the two rivals in decades over the past four days.
When India attacked targets in Pakistan and Pakistan-managed Kashmir, using drones, missiles and artillery began in response to the deadly radical attack in Pahalgam last month. Pakistan denies any involvement.
After four days of cross-border strikes, India and Pakistan said they had reached a comprehensive and immediate ceasefire to reach a consensus.
U.S. President Donald Trump made the announcement on his truth social platform Saturday morning. He said it was facilitated by the United States.
Pakistan's Foreign Minister later confirmed that the two countries had reached an agreement, adding that the "three strikes" were involved in diplomacy.
But hours after the announcement, residents - and BBC reporters - reported in the Kashmiri cities of Srinagar and Jammu, mainly managed by India, that explosions were heard and flashes in the sky were seen.
Indian Foreign Minister Vikram Misri said: “In the past few hours, it has repeatedly violated the understanding we had gained earlier tonight.
“This violates the understanding drawn earlier today.”
Misri said India's armed forces were "providing appropriate responses" and he concluded by "calling Pakistan to resolve these violations".
In response, a spokesperson for the Pakistan Foreign Ministry said: “Pakistan remains committed to faithfully implementing the ceasefire between Pakistan and India.
“Although India has committed violations in some areas, our forces are dealing with the situation with responsibility and restraint.
“We believe that any issues of the ceasefire should be addressed in the appropriate level of communication.
“The forces on the ground should also exercise constraints.”
Kashmir is claimed by India and Pakistan, but is managed only in part by each person, as they were divided after independence from Britain in 1947.
This is a flash point between two nuclear-armed countries, and they fought two wars on these two wars.
Indian Foreign Minister S Jaishankar confirmed the ceasefire, saying the two countries "have some understanding of the cessation of fire and military operations".
He added: "India has always maintained a firm and uncompromising position on all forms and forms of expression. It will continue to do so."
Later, Pakistani Prime Minister Shehbaz Sharif said in his speech to the country that the ceasefire had been reached "in the interest of all".
U.S. Secretary of State Marco Rubio spoke after the ceasefire announcement that India and Pakistan have agreed to start negotiations on a wide range of issues in neutral locations.
He said he and U.S. Vice President JD Vance spent 48 hours with senior Indian and Pakistani officials, including their respective prime ministers Narendra Modi and Shehbaz Sharif.
UN Secretary-General Antonio Guterres said he welcomes "all efforts to reduce conflict".
British Prime Minister Sir Kyle Stemmer said Britain had "participated in" the talks "one day" with Foreign Secretary David Lammy talking to both sides.
"I'm glad to see there is a ceasefire today," Sir Kyle said. "The task now is to make sure it's lasting and lasting."
The latest battle follows two weeks of tension after the killing of 26 tourists in the resort town of Pahalgam.
Survivors of the Kashmir attack managed in India on April 22 killed 25 Indians and a Nepalese national, who said militants were picking out Hindu men.
India's defense ministry said its strike this week was part of a "commitment" to those responsible for the attack. Pakistan describes them as “no reason”.
Pakistan said that since Wednesday, air strikes and cross-border fires in India have killed 36 people in Pakistan, which has occupied Kashmir, while Indian troops have reported that at least 21 civilians were killed in Pakistan shelling.
Fighting intensified overnight on Friday, with the two countries accusing each other of targeting air bases and other military sites.