Britain's most secretive court is to hold a rare public hearing to decide whether there is any legal force behind the long-standing political doctrine that the country's intelligence agencies cannot bug the phones or spy on the emails of members of parliament.

The Investigatory Powers Tribunal agreed to the hearing after two Green party parliamentarians – Caroline Lucas, MP for Brighton Pavilion, and Lady Jones of Moulsecoomb – complained that disclosures by the whistleblower Edward Snowden made it clear that GCHQ was capturing their communications in breach of the so-called Wilson Doctrine.

Kate Grange, counsel for GCHQ, MI5 and MI6, told the IPT on Tuesday that her clients wanted to reserve the right to make submissions on the issue in "closed" – or secret – session, with the public and the media excluded. "It may well be that we would want to say something in closed about the past policy or practice in relation to the Wilson Doctrine," she said.

The convention is named after former prime minister Harold Wilson, who pledged in 1966 that MPs' and peers' phones would not be tapped. In December 1997, then prime minister Tony Blair said the doctrine extended to electronic communication, including emails.

Prime ministers have the power to reverse the policy. While they must inform MPs of the change, they can choose when to announce it. Lucas and Jones argue that the Wilson Doctrine must have legal force, and complain that GCHQ's bulk interception of electronic communications must be unlawful.

The president of the tribunal, Mr Justice Burton, said he wished first to give a judgment on whether or not the doctrine had legal force. At that point, he said, if it did have legal force "we will make our usual inquiries" of the agencies to establish whether the parliamentarians' communications had been intercepted.

Burton raised objections to the agencies' suggestion that the issue may need to be considered partly in closed session, on the grounds that it would fuel criticisms that the IPT operated in a Kafkaesque fashion, which he said it did not.

But he declined to provide lawyers for Lucas and Jones with a copy of an order that the tribunal had issued to the agencies after the parliamentarians' complaint had been lodged. The government's lawyers say they will neither confirm nor deny the existence of the interception programmes that were disclosed by Snowden.

The hearing was adjourned until October.

The IPT investigates complaints about the intelligence agencies and other bodies that have powers of surveillance. Almost all of its work is conducted behind closed doors, with complainants usually unaware that hearings are taking place.

This year the Guardian disclosed [http://www.theguardian.com/politics/2014/mar/05/independence-ipt-court-mi5-mi6-home-office-secrecy-clegg-miliband]that although the IPT claims to be independent of government, it had been secretly operating from within the Home Office since it was established 14 years earlier.

The IPT is also about to hear a challenge to the legality of the government's bulk interception practices, in a case brought by almost a dozen British and international rights groups.

It is also considering a complaint by a Libyan dissident who was kidnapped in 2004 and delivered to Muammar Gaddafi, along with his heavily pregnant wife, with the help of MI6. He alleged that the bulk interception operations had collected his legally privileged communications with lawyers who are bringing his damages claim against the British government and the former foreign secretary Jack Straw.

The IPT has dealt with about 1,500 complaints since it was established. It has not upheld any complaints about any of the UK's intelligence agencies.