The Commonwealth Government is to join court action against Green Senator Bob Brown over logging the Weilangta Forest on Tasmania's east coast, but to a lesser degree than it wanted.

Senator Brown has gone to the Federal Court to try to stop logging in the area because he fears for the habitat of a number of endangered species.

The Commonwealth decided to join the legal case on the side of Forestry Tasmania this month because it fears Senator Brown's actions could challenge the Regional Forest Agreement.

Today the Commonwealth's application to become a party in the proceedings was rejected by Federal Court Justice Shane Marshall.

But Senator Brown's instructing solicitor, Roland Brown, says the Commonwealth will be allowed to intervene, which means it can present arguments to the court.

"It may be allowed to cross-examine witnesses but it's not allowed to file any pleadings, it's not allowed to raise issues in the case," he said.

The State Government has been given another day to register its submission to also intervene in the case on the side of Forestry Tasmania.