No one in the hedge fund community would risk saying it publicly, but some hedge fund money managers are claiming the Securities and Exchange Commission is on a vendetta against the $1.2 trillion industry.

In the past few weeks, the SEC has launched three stock trading investigations that until now have gone unreported. Also, the commission has increased its scrutiny of one of the city’s leading short sellers, Rocker Partners, which has already been sued for alleged stock manipulation.

Summing up the thinking of some hedge fund managers, one manager says there seems to be a mindset at the SEC that anyone who shorts a stock (betting its price will fall) is un-American or crooked. He says he has been hearing ever more complaints from fellow managers about an increase in calls from the SEC that center chiefly on short trades. He points out that such trades are perfectly legal.

Likewise, he says, he and one of his cousins, who works for another hedge fund, have received a number of calls from the commission about what appears to be insider trading investigations. He says such queries were totally unjustified.

Specific SEC questioning, I’m told, centered on possible relationships with analysts, whether conversations were held with any member of the press, and the extent, if any, to which they may have discussed their shorts with two prominent short-selling firms recently in the news.

The SEC’s stepped-up inquiries of hedge fund managers comes amid widespread reports that it is looking into charges and counter-charges involving issuers, short sellers, and research firms.

One brokerage compliance official with strong SEC ties told me the commission is particularly interested in the knack of some hedge funds – notably on stocks they’re short – in influencing analysts to downgrade their investment ratings and in getting financial reporters to do negative stories. He said there is some SEC concern that these incidents are happening in excess – and that the same cast of characters often is involved.

The commission, I’m told, is honing in on the activities of Rocker Partners. It has recently made some calls to the brokerage community specifically seeking information about the firm. Its founder, David Rocker, part of whose success is believed by some hedge fund managers to be his repeated ability to get his short sales publicized in the press, didn’t respond to calls seeking comment.

In recent court action involving allegations of hedge fund stock manipulation, Banc of America Securities LLC and hedge fund SAC Capital Management LLC late last week were named as defendants in a $4 billion class action lawsuit. SAC Capital was charged with “paying, pressuring and otherwise influencing purportedly independent analysts to disseminate materially false and misleading information” about Biovail Corporation as part of a “short selling attack” on the company, a Canadian based maker of drug-delivery systems.

The suit was filed on behalf of Biovail shareholders against defendants such as SAC Capital’s founder, Steven Cohen; an independent research firm based in Scottsdale, Ariz., Gradient Analytics, and a Banc of America analyst, David Maris. The SEC already is investigating the allegations in the Biovail lawsuit.

In another action, Rocker Partners was sued last August by online retailer Overstock.com for short selling the company’s shares and conspiring with Gradient to denigrate its business for a profit. Gradient, which was also sued, “knowingly served as a shill for Rocker Partners,” Overstock.coms aid in its suit, which seeks unspecified damages.

The SEC within the past three weeks has initiated three new stock trading investigations, presumably centering on the misuse of inside information. They involve:

* Bausch & Lomb, a leading maker of contact lenses and lens care solutions. On March 26, a class action lawsuit was filed on behalf of all persons who purchased the company’s shares last year between January 27 and December 22. The complaint alleges Bausch & Lomb violated securities laws by issuing a series of materially false statements concerning its results.

* Taser International, a controversial stun gun maker that has had previous run-ins with the SEC.

* USG Corporation, a $5.1 billion manufacturer of construction materials.

The SEC, which is soliciting the names of brokerage customers who have traded in the stocks and options of these three companies, won’t comment on individual investigations, but a regulatory official confirmed all three probes.

In another regulatory development, the New York Stock Exchange as of March 24 has begun an investigation into the trading in the shares of money manager GAMCO Investors. At the same time, the Justice Department is pursuing claims against the firm’s CEO, Mario Gabelli, for allegedly participating in a Federal Communications Commission license scam in the mid-1990s. Mr. Gabelli is fighting the allegations. An NYSE spokeswoman declined comment.

An SEC spokesman, John Nester, also declined comment when asked about charges from the hedge fund community that the commission is on a vendetta against such funds.