Detective sergeant Steve Santorelli, a senior detective at Scotland Yard's computer crime unit, said some ISPs have been turning down legitimate requests for help in tracing hackers and virus writers.
"The problem is that ISPs are in a commercial business and they see no pound value in co-operating with the police," he said. "It is a problem that we are going to face constantly as time goes on. Short of a change in the legal system, we have to rely on their good will."
The disclosure will raise questions about the adequacy of the Single Point of Contact (Spoc) system, used by police and other law enforcement agencies to channel requests for data, known as section 29.3 notices, to internet and telephone companies.
The computer crime unit said it is often easier and quicker to secure information needed for investigations from overseas ISPs than from some UK firms.
"There is one particular ISP that recently declined to release details of a subscriber with a particular internet address because we were not investigating an incident involving terrorism or paedophilia. That is unacceptable for everyone when our core business is investigating hackers and virus writers," said Santorelli.
Scotland Yard said it was in the interests of ISPs to co-operate in investigations against hackers and virus writers, as they often fall victim to attacks themselves.
"If an ISP gets a reputation for not co-operating with the police, that is going to damage their business. Can you imagine the impact it would have if an ISP gets a reputation as the ISP of choice for black hat hackers?"
The London Internet Exchange, which represents 130 ISPs, said it was not aware of any cases of ISPs being unco-operative but it would be willing to discuss the matter if police were experiencing problems.
"The ISPs can only respond to correct documentation from the Regulation of Investigatory Powers Act and the process that needs to be followed. We are not aware of any ISP that has refused to co-operate when that documentation has been given to the ISP," it said.