Prime Minister John Howard denied yesterday bullying East Timor over a lucrative gas project as Parliament passed the crucial Timor Sea Treaty.

The laws, rushed through on the last sitting day before a March 11 deadline to ratify the treaty, underpinned the $3 billion Bayu-Undan gas development in the seabed shared between Australia and the fledgling nation.

In the Senate, Greens Leader Bob Brown accused Mr Howard of blackmailing the East Timorese into signing a deal on the larger Greater Sunrise field, or risk losing the Bayu-Undan deal. Senator Brown was suspended from the Senate when he refused to withdraw the comments.

Mr Howard strongly denied threatening to scuttle the Bayu-Undan development unless the East Timorese ratified a second agreement on the 80 per cent Australian-owned Greater Sunrise gas field.

He had telephoned East Timorese Prime Minister Mari Alkatiri yesterday to ask whether the unitisation agreement on Sunrise could be ready to be signed by the afternoon, Mr Howard said.

"Allegations were made by Senator Brown that I have sought to intimidate, to strong-arm the East Timorese leadership over the Timor Sea negotiations – both claims are totally false," Mr Howard told Parliament.

"My call to Dr Alkatiri, which was totally civil and cordial in accordance with our close relationship, related solely to formal processes, and not to any of the substance of the negotiated package."

The unitisation agreement, which determines East Timor's share of Greater Sunrise revenue based on the 20 per cent of the field that lies in the shared zone, had been finalised at the weekend, Mr Howard said.

The Timor Sea Office, which negotiates for Dr Alkatiri on gas and petroleum issues, accused Australia of applying unnecessary and disrespectful diplomatic pressure on the East Timorese government to sign off on Sunrise.

Foreign Minister Alexander Downer denied East Timor was bullied but said lively discussion had led to a fair compromise between Australian and East Timorese interests. Mr Downer flew to Dili to sign the Sunrise agreement late yesterday.

A partial transcript of Mr Downer's negotiations with the East Timorese appeared on the crikey.com.au web site, which accused yesterday the Foreign Minister of behaving like a pompous colonial git in the negotiations.

But the Department of Foreign Affairs and Trade said the transcript was clearly a translated and edited version of the negotiations, and denied the document had come from within the department.

The Greens and Australian Democrats also accused the Government of ambushing the Senate by allowing a single day for the treaty laws to be passed.