Khan told Macron that the actions taken by India "posed a grave risk for peace and security" in the region, the Prime Minister's Office said in a statement.
"I will also speak to Pakistan Prime Minister after a few days and tell him that the talks should be held bilaterally," Macron had said in a joint press statement after his talks with Prime Minister Narendra Modi on Thursday.
On Wednesday, President Macron told Khan to resolve all outstanding issues "through peaceful means," the statement said.
Separately, Khan called King Abdullah of Jordan and discussed the situation in Kashmir.
King Adbullah called for de-escalation of the situation and stressed for peaceful resolution of the Kashmir dispute through dialogue.
Meanwhile, Foreign Minister Shah Mahmood Qureshi wrote another letter to the President of the UN Security Council to highlight the developments in Kashmir.
The Foreign Office said that Qureshi referring to the Security Council meeting of August 16 reiterated Pakistan's concerns about "India's irresponsible and belligerent rhetoric on the nuclear issue".
The rare closed-door consultations on Kashmir by the Security Council on August 16 ended without any outcome or statement from the powerful 15-nation UN organ, dealing a huge snub to Pakistan and its all-weather ally China to internationalise the issue, which an overwhelming majority stressed is a bilateral matter between New Delhi and Islamabad.
Qureshi underscored Pakistan's readiness to cooperate in every possible way with the Security Council, the Secretary General and the world community to promote a peaceful resolution of the Kashmir issue, the FO said.
(with inputs from PTI)