The Cape Wind project generated enough controversy to prompt some 40,000 comments to be submitted to the Minerals Management Service, setting a record at the agency.

By the time federal regulators stopped accepting public comments about the proposed Nantucket Sound wind farm on Monday, two of the letters had already raised some eyebrows among the project's critics. That's because the two letters were signed by the same person, state Division of Marine Fisheries director Paul Diodati, but they struck noticeably different tones.

The first letter, which was dated Feb. 20, recaps many of the fishing industry's concerns. While the sound's Horseshoe Shoal section is nowhere near as busy as the heavily fished parts of Georges Bank or Massachusetts Bay, some fishermen rely on the shoal to catch a range of critters, including sea bass, flounder, squid and conches. The fishermen worry that 130 giant wind turbine towers spread over 24 square miles could jeopardize those catches.

Diodati's first letter spells out the loss of access that fishermen could face as well as concerns about rescue crews reaching a troubled boat in the area.

But the second letter, dated March 7, tones down the rhetoric considerably, reducing the section that lists the potential impacts to fisheries to just a few sentences. The section also mentions a couple of possible benefits, such as certain species becoming attracted to the newly built tower foundations.

Neither letter mentions the stance of Diodati's boss, Gov. Deval Patrick. But the state's fishermen know Patrick was one of the most vocal supporters of Cape Wind when he campaigned for governor in 2006.

Tom Osmers, a shellfish constable in West Tisbury, says he was disappointed by the shift in tone. However, he also says the state agency is probably focusing on mitigation efforts with the understanding that the project is going to happen anyway. "They're just trying to make the best of what they seem to think is inevitable," Osmers says.

But Ed Barrett, a Marshfield fisherman who is president of the Massachusetts Fishermen's Partnership, says he sees the long arm of Patrick's politics at work in the Division of Marine Fisheries. "It's pretty obvious that someone told them that they were going to look the other way," Barrett says.

Diodati, for his part, denies that Patrick or his top aides interceded on the issue. He readily admits that there is a change in tone between the letters, but says that shift was intentional.

Diodati explains the change this way: His agency had initially thought the deadline for commenting on the project was Feb. 20. He was out of the state on vacation with his family that week, but worked remotely with his staffers to pull together a submission that reprised many of the agency's previous comments.

When Diodati returned to the office and learned that the comment period had not expired, he says he met with his aides to take a more thoughtful approach.

"We actually wanted to say things that could be done to actually improve the project, rather than say we think this is a problem," Diodati says. "They might be different in tone. In fact, I hope there is, because that was our intent."

Diodati says he figures that his agency's concerns with the project clearly had been spelled out in previous regulatory filings. The agency, he says, hasn't changed its opinion about any of those previous concerns.

Mark Rodgers, a spokesman for project developer Cape Wind Associates, says he's not surprised by the changes between the letters. He says they mirror a changing attitude among federal fishing regulators as they realize that the project's effect on fishing won't be severe. He says Cape Wind's research shows that only about 4 percent of the sound's entire fishing catch comes from Horseshoe Shoal.

But Barrett's group submitted its own study, which estimates that $8 million to $13 million could be lost to commercial fishermen over the life of the project. While the developer says Horseshoe Shoal will stay open for commercial fishermen, Barrett says most trawlers will steer clear because of the navigation hazards posed by the windmills.

That's just one example on a long list of differing opinions about the project's potential impacts. It's hard to know how the folks at the MMS will be able to review all 40,000 comments and make a final decision this year.

But some letters are going to stand out among the sea of submissions. Diodati can rest assured that his agency's comments will be among them.