Police are questioning two boys over the recordings of calls made to Scotland Yard's Anti-Terrorist Hotline.
The suspects, aged 16 and 17, are being held in the West Midlands by detectives from the Police Central e-Crime Unit.
They were arrested last night on suspicion of offences under the Malicious Communications Act and the Computer Misuse Act.
A Scotland Yard spokesman said the pair were in custody in the West Midlands.
An anarchist group known as Team Poison has claimed it eavesdropped on highly-sensitive counter-terror conversations after bypassing technology from the 1980s.
A number of recordings were posted on YouTube by the group.
The Met said the Police Central e-Crime Unit (PCeU), which is leading the investigation, was aware hoaxers had made calls to the hotline and made recordings of their conversations with anti-terrorist hotline staff.
An earlier statement said: "The Anti-Terrorist Hotline remains operational and we continue to urge members of the public to report any suspicious activity to the police.
"Public reporting is an important part of the fight against terrorism and any attempt to disrupt this service will be investigated thoroughly."
Before the arrests Ailsa Beaton, director of information at Scotland Yard, said she was satisfied there was no attack on internal systems.
"We have throughout the day researched the allegation that the Anti-Terrorist Hotline had been 'hacked' and activists' claims that they were able to listen unrestricted to confidential communications," she said.
"We are confident the MPS communication systems have not been breached and remain, as they always have been, secure.
"We are satisfied that any recording would have been made via the receiving handset only and not from an attack on internal systems.
"The public can remain confident in the ability to communicate in confidence and that the integrity of the Anti-Terrorist Hotline remains in place."