But the BBC's Sola Odunfa in Lagos says there were no witnesses to the killing and so investigations may take some time.
The mutilated body of Maria Theresa Nsa was found at her home on 11 June.
She had been "hacked to death", a police spokesman was quoted as saying by the French news agency, AFP.
She may have been killed in revenge for denying a group of murder suspects bail, the police spokesman said.
No protection
The suspects were being held in connection with the murder in Cross River State last year of a local government councillor.
The police spokesman said that a political motive for the murder of the magistrate could not be ruled out.
"We cannot rule out a political motive for her assassination. She gave a ruling about some notorious criminals and a few hours later, she was dead," he said.
Our correspondent says the murder raises once again the issue of the personal security of public officials such as judges and magistrates who undertake serious civil and criminal cases.
There have been a number of attacks on members of the judiciary in recent months but they are not accorded police protection at their homes, unlike prominent political figures who often have armed police escorts.
He told the BBC's Network Africa that the police are short-staffed and are unable to provide protection for all public officials who may need it.
Accustomed
"The police have not solved a single case of assassination in five to 10 years," he said.
The then Justice Minister Bola Ige was shot dead by armed gunmen last December.
Sola Odunfa says that sadly, Nigerians are becoming used to the assassination of public officials.
The Chairman of the Calabar branch of the Nigerian Bar Association, Joe Agi, called for an official investigation into the killing of Ms Nsa and said his association would set up its own "independent" inquiry.
"The police should leave no stone unturned to get the culprits," he said.
Courts in Calabar have not held any sittings since news of the chief magistrate's death was announced on Wednesday.