Mail & Guardian editor Nic Dawes and two of the newspaper's journalists were questioned at the specialised commercial crimes unit in Pretoria on Thursday.
"We were asked to attend what is called 'warning' interviews," Dawes said.
"This is a formal process, in terms of which you are informed of the charges brought against you and you are advised of your rights. You are also given the opportunity to make a statement or ask questions," he said.
Dawes said charges laid against himself, Sam Sole and Stefaans Brummer related to contravention of Section 41 (6) of the National Prosecuting Act of 1998.
It dealt with records collected by the NPA in the course of a confidential inquiry.
He said there was also a charge of theft of the records.
Presidential spokesman Mac Maharaj laid criminal charges against the Mail & Guardian in November last year. The case was handed over to the Hawks.
Maharaj has accused the newspaper as well as Sole and Brummer of violating the NPA Act.
The charges relate to a front page story in the newspaper which featured a picture of Maharaj, alongside the words: "Censored. We cannot bring you this story in full due to a threat of criminal prosecution."
Big black blocks were printed over about three-quarters of the page, where the story would have been published.
Maharaj contended the decision by the newspaper to black out parts of its report had created the impression that he had done something wrong.
He said the act made it an offence to disclose evidence gathered in camera by a Section 28 inquiry.
According to the newspaper, Maharaj had lied to the Section 28 inquiry called by the now disbanded Scorpions over allegations that he received kickbacks from French arms manufacturer Thales International.
It was this information, allegedly proving that Maharaj had lied, that the newspaper wanted to publish.
Maharaj has denied ever being involved in corruption and bribery.
Dawes said on Thursday the next step in terms of the investigation was that a decision would be made on whether to pursue prosecution.
"We will see how things unfold from here. Obviously our concern is [that] it is a very serious criminal charge, which carries a 15-year jail sentence," said Dawes.
"[This] is being used to prevent journalists from dealing with really important matters that are in the public interest."
There were similar provisions in the Protection of State Information Bill.
"This case makes it clear why we have concerns," he said.
Dawes said when the newspaper was originally informed that it would be an offence to publish the information it made a formal request to do so, but this was denied.
The Mail & Guardian had since launched a formal High Court application to have the decision reviewed.
"We believe some of the info[rmation] is in the public domain and in the public interest. That court application will continue to unfold," said Dawes.