"A serious kidnap incident happened in the Philippines. Hong Kong residents should avoid all travel to the country," a government spokesman said in a statement.
"Those who are already there should attend to their personal safety and exercise caution."
At least 8 of the hostages have been killed while 7 others were being treated in hospitals after their 12-hour ordeal, police and doctors in Manila said.
The Hong Kong government also said it would charter two flights to Manila for families of the tourists who were held hostage by an armed ex-policeman in their tourist bus.
Andy Ho, spokesman for Hong Kong Chief Executive Donald Tsang, said the city's airline Cathay Pacific will arrange two chartered flights for family members, as well as psychologists, immigration and medical officers.
The first flight will take off around midnight on Monday (1600 GMT) and the second flight is scheduled for 8 am on Tuesday, he said.
"We are ready to go but we are awaiting landing permission from Manila," Ho said.
The busload of Hong Kong tourists was seized by former senior police inspector Rolando Mendoza, who said he wanted to clear his name after being discharged for extortion in 2008.
The gunman was killed by police in the final moments of the crisis.In Manila, the Chinese embassy said it was saddened by the death of the hostages. It asked the government to attend to the survivors.