Modi, who arrived here this morning, held the meeting at Jammu's Technical Airport and was briefed by Abdullah on the devastation caused by the floods which have claimed 116 lives, officials said.
The Prime Minister is scheduled to undertake an aerial survey of the flood-hit areas in Jammu zone, they said.
He will later fly to Srinagar for an assessment of the damaged caused by the floods.
The decision on the Prime Minister's visit came following a review meeting which he called after being briefed yesterday by Home Minister Rajnath Singh who returned to the national capital after surveying the flood-affected regions, the Prime Minister's Office had said in a statement.
"After reviewing the situation, the Prime Minister decided to visit Jammu and Kashmir to personally assess the gravity of the situation and understand the problems being faced by the people," it had said.
The Cabinet Secretary and Modi's Principal Secretary were among those who had attended the meeting.
Torrential rains which triggered flooding, landslides and house collapses have so far claimed 116 lives.
Modi, while condoling the deaths in the flood, had on Thursday announced Rs 2 lakh as ex-gratia relief for the kin of the deceased and Rs 50,000 for the seriously injured.