When the National Oceanic and Atmospheric Administration closed down Sector IX to groundfishing back on November 20, many felt the organization was punishing New Bedford fishermen for the actions of "The Codfather" Carlos Rafael. It was Rafael's vessels that went over catch limits as part of his overfishing scheme that sent him to federal prison.

NOAA regional administrator John Bullard told WBSM News that shutting down the sector isn't about any kind of sanctions or punitive actions for Rafael's scheme, but rather for cleaning up the mess he left behind.

"The basic responsibility of a sector is to report the catch, and to keep vessels within the limits for that sector for all the species of groundfish," Bullard said. "To this date, we don't know how many fish the vessels in Sector IX have caught. We don't know how much they have exceeded the limits on some of their catch, and we think some of those overages are significant."

Bullard said that since 2012, when NOAA went to the quota-based system, it has been each sector's responsibility to keep track of its own catch.

"They can lease back and forth within a sector, they can lease fish from one sector to another," he said. "That's all designed to maximize efficiency and keep government kind of out of it, and allow the efficiency of the private sector to work. Mr. Rafael misused that system, and until we understand how much they went over and what species, we're not about to let the boats go fishing again."

Bullard said NOAA initially reviewed the sector's operation plan back in May along with those of all the other sectors, as the fishing year begins on May 1.

"I decided at that time, that even though there were problems with Sector IX last May, we would allow them to continue operating because the trial had not taken place. We felt we should let them operate until the trial concluded," he said. "We faced a lot of criticism for that decision."

But once the trial was completed and Rafael was sentenced to about four years in prison, the decision was made to halt operations in Sector IX until the extent of the overfishing could be determined. As part of the shut down, the Sector IX vessels cannot join other sectors, or the common pool.

Back in December, the new board of Sector IX sent a letter to Bullard stating they had complied with NOAA's requests to bring in new board members and begin properly reporting their catches, and therefore should be allowed to continue fishing. Bullard said it's not as simple as that, although he called revamping the board "a significant step in the right direction."

"But the problems with Sector IX are significant, and wide-ranging, and they're not going to be corrected by just a new board," he said. "We have to understand how much in debt, if you will, the sector is, how much they went over, because before they can operate, those debts are going to have to be repaid."

While some have tried to portray Bullard, the former mayor of New Bedford, as the villain in this situation because his decision is keeping about 80 or so fishermen from making a living, he said that's to be expected--but people shouldn't forget it's Rafael who caused this situation.

"I know that's the way people look at it," he said. "But Mr. Rafael has victimized people in New Bedford for many years. To hear him profess about the people of New Bedford is galling, to say the least."

"I would lay the blame with Mr. Rafael. He's the criminal in all of this, and we're trying to clean up the mess that he has created."

Mayor Jon Mitchell recently estimated that groundfishing and shoreside businesses affected by the shutdown are losing about a half-million dollars a day. Bullard didn't deny that estimate, but noted that Mayor Mitchell frequently points out that New Bedford is the largest dollar port in the country by far, and has a lot of economic activity that can absorb some of that hit.

"As significant as Mr. Rafael's enterprise was economically, it was overshadowed by all the other economic activity in the fishing industry in the city of New Bedford," Bullard said. "The scallop activity, the red crab activity, the surf clam and the ocean quahog, other groundfishing, offshore lobster. There's a lot going on in the port of New Bedford. It's a very healthy port."

"I don't want to minimize that people are suffering, because some people are, but there's a lot of fishing activity in the port of New Bedford that's not related to Carlos Rafael," he said.

Bullard said his staff has met with the new Sector IX board, and he himself has also met with one of the board's representatives. He also said he heard a number of people testify at the New England Fisheries Council meeting in Newport a few weeks ago, and that there are plans to meet with the Sector IX fishermen early in the new year.

Bullard said he's not going to be offering any kind of time table on a return to the seas for the fishermen.

"I just don't want anyone thinking this will all be over in a matter of weeks," he said. "It's going to take a lot longer than that."

He also said he has not heard anything about what will happen to the vessels and permits owned by Rafael, which Mayor Mitchell has suggested he be allowed to sell to interested parties in New Bedford as part of his forfeiture agreement with the federal government.

Bullard said it's still going to take time to figure it all out, even with Rafael now behind bars.

"I understand that not being able to fish is difficult. We're very much aware of that. But we do have a job to do," Bullard said. "I'm very sorry for the people that it affects, but it's Mr. Rafael's mess that we're trying to clean up."