The head of the state maritime authority was unaware his deputy was in regular phone contact with then NSW Labor MP Eddie Obeid and only found out after the fact the senior bureaucrat had met a mediator representing Obeid family business interests, the Supreme Court has heard.

Mr Obeid, 72, is standing trial for misconduct in public office for failing to disclose his family had an interest in two cafe leases at Circular Quay when lobbying Steve Dunn, then deputy chief executive of the NSW Maritime Authority, about the plight of waterfront leaseholders.

The former upper house MP has pleaded not guilty to the charge.

Chris Oxenbould, the former chief executive of the maritime authority, gave evidence on Friday he was aware Mr Obeid and Mr Dunn had struck up a friendship when the former was fisheries minister and the latter was the head of the fisheries department.

He said he was aware they "occasionally met" for coffee but he did not believe it was related to the maritime authority's business.

Mr Oxenbould was also aware they spoke on the telephone, but only discovered the extent of the contact later.

"I thought it was far more occasional and infrequent," Mr Oxenbould said.

The court has heard Mr Obeid did not reveal his family had an interest in cafes on wharves four and five at Circular Quay when he asked Mr Dunn, who is not accused of any wrongdoing, to meet a commercial mediator in 2007.

The mediator was acting for an Obeid-linked company, among others, to secure a renewal of harbourside retail leases without competing in a public tender.

The defence says Mr Obeid did "no more" than ask Mr Dunn to meet the mediator and did not advocate any particular outcome.

Asked if he would have expected to have been informed of the meeting between Mr Dunn and the mediator, Mr Oxenbould said: "Yes, I would have."

He said that as a matter of general practice it "would be very unusual for a member of parliament to be making an enquiry directly" of a senior bureaucrat in a government agency without the involvement of the relevant minister.

Mr Oxenbould said there had been some "rumour and innuendo" within the department that Mr Obeid's family had an interest in Circular Quay leases.

"It was never put to me seriously as a fact," he said.

Had he known of the interest, Mr Oxenbould said would have informed the minister and would have been "more alert to the outcomes of various meetings that were taking place".

The trial continues.