He added that the detention was a “deliberate attempt to influence the outcome of elections” in three weeks.
Mr Adams is being questioned about the 1972 murder of Jean McConville but has denied involvement in her death.
Prime Minister David Cameron said there had been “absolutely no political interference in this issue”.
Northern Ireland First Minister Peter Robinson said it would be “political policing” if Mr Adams was not questioned.
The Sinn Féin president remains in custody after presenting himself at Antrim police station on Wednesday evening.
Mr McGuinness, Northern Ireland’s Deputy First Minister, told a press conference at Stormont that the arrest of his party leader and “friend” was politically motivated.
He claimed Sinn Féin had been told by “senior” and “reforming” figures within the Police Service of Northern Ireland (PSNI) that “there was still a dark side within policing here in the north of Ireland”.
“I think we have seen that dark side flex its muscles in the course of the last couple of days,” he added.
“We know who they are. The reformers know who they are,” Mr McGuinness told reporters.
He said some former republicans who were “maliciously and vehemently hostile to the peace process” had been targeting Mr Adams and the Sinn Féin peace strategy for a considerable period of time.
“It is quite disappointing to see the efforts of those people now in consort with the dark side within policing,” Mr McGuinness said.
However, Mr Robinson said the arrest was proof that no-one in Northern Ireland was above the law.
“Is anybody going to say to me that if the police are aware of claims and evidence in relation to such a barbaric killing that it would be political policing for them to question those who have been suggested to have been involved?
“I would suggest to you that it would be political policing if the PSNI had not questioned those that were deemed to have been involved in any way,” the DUP leader said.
“I cannot say whether Mr Adams will be charged or released, whether he will be held for a further period, whether even if charged he might be convicted .
“But what I can say is that it strengthens our 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.”
In a statement, a PSNI spokesman said: “Police have a duty to impartially investigate serious crime including murder.
“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 (PPS), 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.”
Speaking before his detention on Wednesday evening, Mr Adams said he was “innocent of any part” in the murder.
“I believe that the killing of Jean McConville and the secret burial of her body was wrong and a grievous injustice to her and her family,” he added.
Mrs McConville, a 37-year-old widow and mother-of-10, was abducted and shot by the IRA.
Her body was recovered from a beach in County Louth in 2003.
Mrs McConville’s son Michael, who was 11 when his mother was murdered, welcomed the arrest.
“We’re just happy to see everything moving as it is moving at the minute,” he said.
“Me and the rest of my brothers and sisters are just glad to see the PSNI doing their job. We didn’t think it would ever take place [Mr Adams’ arrest], but we are quite glad that it is taking place.”
Mrs McConville, one of Northern Ireland’s Disappeared, was kidnapped in front of her children after being wrongly accused of being an informer.
The claim that she was an informer was dismissed after an official investigation by the Northern Ireland Police Ombudsman.
The widow was held at one or more houses before being shot and buried in secret.
The Disappeared are those who were abducted, murdered and secretly buried by republicans during the Troubles.
The IRA admitted in 1999 that it murdered and buried at secret locations nine of the Disappeared.
The Independent Commission for the Location of Victims’ Remains was established in 1999 by a treaty between the British and Irish governments.
It lists 16 people as “disappeared”. Despite extensive searches, the remains of seven of them have not been found.
Jean McConville’s remains were found in 2003 by a man walking at Shelling Hill beach, near Carlingford.
Last month, Ivor Bell, 77, a leader in the Provisional IRA in the 1970s, was charged with aiding and abetting the murder.
There have also been a number of other arrests over the murder recently.
Mr Adams has never been charged with membership of the IRA.
He was, however, interned in 1972 under the controversial Special Powers Act, but briefly released in order that he could take part in talks in London between representatives of Sinn Fein and the then Home Secretary Willie Whitelaw.