A curfew has been imposed in Indian-administered Kashmir following a day of violence on Wednesday in which at least eight people were killed.
India and Pakistan have meanwhile exchanged bitter recriminations as to who was responsible for the violence.
Earlier on Wednesday, militants killed five security personnel in a gun and grenade attack in the city.
The curfew was imposed after a man was killed later in the day in clashes between police and protesters.
Indian Home Secretary RK Singh said two gunmen killed in the attack appeared "not local but from across the border" - a reference to Pakistan.
But the foreign ministry in Islamabad issued a statement late on Wednesday which rejected Mr Singh's accusations.
The statement also rejected claims by India that Pakistani troops beheaded two Indian soldiers on 8 January - the last time the two sides exchanged accusations over the long-running Kashmir conflict.
"We feel that this trend of making irresponsible statements and knee-jerk reactions by senior Indian government functionaries have the potential of undermining the efforts made by both sides to normalise relations," it said.
Pakistan "condemns such actions of terrorism in the strongest possible terms and calls upon the government of India to carry out a thorough investigation... before levelling such accusations which are counter-productive and serve no purpose."
Life in Srinagar has gradually returned to normal despite the imposition of the night-time curfew late on Wednesday. The Indian authorities have not said when it will be lifted.
Police and soldiers have been deployed in the city to maintain calm.
The two gunmen attacked a security camp manned by the Central Reserve Police Force (CRPF) in the Bemina district of Srinagar. At least 11 people including four civilians were injured.
It was the bloodiest militant attack for three years in the region, which is claimed by both India and Pakistan.
Later in the day, a vehicle carrying security forces allegedly opened fire on a group of protesters in the Zoonimar area, killing Mohammad Altaf Wani, police said.
But local media quoted eyewitnesses as saying that Mr Wani and his uncle were on their way to work when they were allegedly shot at by the security forces. The uncle escaped unhurt.
Indian-administered Kashmir has seen an insurgency against Indian rule since 1989, but violence has declined in recent years.
The Hizb-ul Mujahideen militant group said it had carried out the attack and threatened more violence, according to local media reports.
The BBC's Riaz Masroor in Srinagar says that the attack was the most high-profile in the city in three years.
Our correspondent says that it came against the backdrop of last month's hanging of Afzal Guru, who was convicted of plotting the 2001 attack on India's parliament.
Many Kashmiris believe Guru did not receive a fair trial and there have been weeks of curfews, strikes and protests.
For years, separatists and rights activists have warned of a revival of militancy in Kashmir.
The dispute between India and Pakistan over who controls the territory has been the spark for two of the three India-Pakistan wars: the first in 1947-8 and the second in 1965.