It comes after the deputy First Minister blamed the "dark side" of policing for the timing of his party leader's arrest in the run-up to the European and local council elections.
Mr McGuinness said: "People who could be described as former republicans (are) targeting the Sinn Féin peace strategy and targeting the leader of Sinn Féin, Gerry Adams.
"It has been disappointing to see the efforts of some of those people together in consort with the dark side within policing."
"That raises very serious questions around why that is the case and what is the agenda," Mr McGuinness added.
But Mr Cameron said: "There has been absolutely no political interference in this issue.
"We have an independent judicial system, both here in England and also we do have one in NI. We have independent policing authorities, independent prosecuting authorities. Those are vital parts of the free country and the free society we enjoy today."
The two men spoke by phone on Thursday evening and Sinn Féin said Mr McGuinness raised the issue of Mr Adams' arrest with the Prime Minister.
He also said there has been "no consistency on the part of the British state" when it comes to investigating state killings during the Troubles and added: "The PSNI is duty bound to fully and energetically pursue all and every investigation and I support and encourage them to do so."
I view his arrest as a deliberate attempt to influence the outcome of the elections that are due to take place in three weeks' time, north and south on this island.
Sinn Féin's Martin McGuinness
Mr Adams is currently still in custody at Antrim PSNI Station where he is being held as part of the investigation into the 1972 abduction and murder of west Belfast mother Jean McConville.
He presented himself voluntarily to the station on Wednesday night where he was then arrested and questioned under caution by detectives from the PSNI's Serious Crime Branch.
UTV understands he is being questioned under the Terrorism Act 2000 and can be held for 48 hours before police need to apply to the courts for additional time to continue their interview.
Mr Adams has always denied having any part in the murder.
Meanwhile the DUP leader and First Minister Peter Robinson has come out in support of the PSNI in the actions they have taken in the McConville murder investigation.
He explained: "I would suggest it would be political policing if the PSNI had not questioned those that were deemed to have been involved in any way.
"It strengthens the political process in Northern Ireland for people to know that no-one is above the law, everyone is equal under the law and everyone is equally subject to the law.
"I commend the police for the action they have taken. They must have known that by taking this step they would be criticised from some quarters but it is my duty as First Minister, as it is for others that have taken up ministerial office, to give their support to police and the rule of law."
The matter was also raised at the Policing Board on Thursday.
Police have a duty to impartially investigate serious crime including murder.
A statement from the PSNI after the meeting said: "It is the police's duty to make relevant enquiries, interview those with information, arrest and question suspects and, in consultation with the Public Prosecution Service, to either charge or submit a file to the PPS in relation to the investigation.
"This procedure is being followed in this case.
"As one individual has been charged with serious offences and files are being prepared in relation to other individuals, it would be inappropriate to comment further other than to reiterate the Police Service's commitment to treat everyone equally before the law."
Dolores Kelly, SDLP MLA, said: "The police made it very clear during the Policing Board that they will go wherever the investigation leads.
"I believe that's what they've done and I don't accept the argument that it was political policing."
Chris Lyttle, Alliance MLA, said: "I think if there's a case to be answered to Gerry Adams has obviously approached the police and I think we need to see due process take its course now regardless of the time of the year that is happening."
Mike Nesbitt, UUP leader, said: "Three things have happened - first of all Gerry Adams has said he'll talk to the police about a very serious murder, secondly thinking about it the police say we would like to do that but then thirdly, the man's best friend accuses the police of a conspiracy.
"What planet is Martin McGuinness on that he is accusing the police of doing something wrong when they're simply accepting an invitation from Gerry Adams?"
Taoiseach Enda Kenny TD said: "This is still an investigation and what I can say is that I hope that that Mr Adams answers in the best way that he can to the full extent that he can about questions that are being asked about a live murder investigation."