Wilbert Sabine was testifying at the judge-only trial of Peter Andrews, the executive director of corporate services for the province's Aquaculture Department.
Andrews has pleaded not guilty to obstruction of justice after he was accused of interfering in an aquaculture investigation in 2011 involving Donat Robichaud, the brother of deputy premier Paul Robichaud.
Sabine said there were previous investigations involving Donat Robichaud before Andrews joined the department, and instead of charges, Robichaud was granted time to follow the regulations.
"He would come into compliance and go out of compliance, back and forth," Sabine told provincial court in Fredericton, adding that the boundaries of Robichaud's oyster operation would sometimes extend too close to shore.
Sabine said the department has always tried to work with aquaculture operators who may be violating regulations and charges are a last resort.
He said in June 2011, he sent an email to fisheries officer Gaetan Germain to again investigate Robichaud's site.
Germain had a package of information ready for Crown prosecutors in October 2011 and responded on Nov. 16, 2011, that the Crown had approved a charge, the court heard.
Sabine said it was standard practice within the department to notify the fisheries minister of any charges, so he told Germain to hold off laying the charge until he gave the OK to proceed.
"We think the minister will want to talk directly with the client's brother," Sabine wrote in the email to Germain, the court heard.
Patrick Hurley, Andrews's defence lawyer, asked why that would be the case. Sabine said he assumed it was just a courtesy.
Sabine said he became aware on Nov. 23, 2011, that senior management of the department was looking for other ways to handle the Robichaud case, such as giving him more time to comply, before revoking his licence or laying a charge.
In February 2012, the Opposition Liberals said they received a letter from an anonymous source alleging that Paul Robichaud interfered with the departmental investigation involving Donat, an allegation the deputy premier has denied.
It was never indicated or said by any superiors that Paul Robichaud gave any directive not to lay charges, Sabine said Monday.
He said though he told Germain on Nov. 23, 2011, not to proceed with charges, Germain did anyway. Sabine said he became aware on Dec. 12, 2011, that the charge was laid.
Sabine said Andrews asked him to call the Crown to see if the charge could be dropped, but prosecutor P.J. Veniot declined.
"'This situation stinks,'" Sabine quoted Veniot as saying during that conversation. "And he wasn't going to have stink stick to him."
Donat Robichaud later pleaded guilty to practising aquaculture outside the boundary of his lease and paid a fine.
The Crown is expected to call at least two witnesses Tuesday.
Andrews is expected to take the stand later this week.