The prime minister's comments came after he visited the military hospital in Jammu, where he met the people injured in the May 14 attack in Kaluchak.
One of the moderate voices in the Hurriyat, Lone was shot dead by unidentified men at a rally to mark the 12th death anniversary of former Mirwaiz of Kashmir, Maulvi Mohammad Farooq, in Srinagar.
Vajpayee said that Lone was working for peace and perhaps that is the reason why he was killed.
The peace process might be affected by the killing, he added.
Earlier, Governor G C Saxena, Chief Minister Farooq Abdullah, Union minister Chaman Lal Gupta and senior army, police and civil officials received Vajpayee at the Jammu air force station.
The prime minister, who will visit Kashmir on Wednesday to assess the situation there, said he would comment on the escalating tension with Pakistan before concluding his trip.
"I will reply before leaving back for Delhi," he said.
Firing at Hurriyat meeting; Lone killed
Lone Interview: If BJP
can't solve the J&K problem; no other party can
Lone Interview: We have fallen into a trap
Islamic extremists are biggest threat in J&K: Lone
Lone welcomes idea of
'core group' on Kashmir
Hurriyat to send Lone to meet Annan
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