NEW YORK - It looks as if the Bowl Championship Series is headed for another major overhaul.

The Associated Press has told the BCS to stop using its college football poll to determine which teams play for the national title and in the most prestigious bowl games.

Since the BCS was implemented in 1998 by officials from the Big East, Big 12, Big Ten, Atlantic Coast Conference, Pac-10, Southeastern Conference and Notre Dame, the formula it uses to rank teams has been tweaked almost every year. But the AP poll and the ESPN/USA Today coaches poll have always been an integral part.

The AP said such use was never sanctioned and had reached the point where it threatened to undermine the independence and integrity of the poll.

The AP sent BCS coordinator Kevin Weiberg a cease-and-desist letter, dated Dec. 21, stating that use of the poll is unlawful and harms the AP’s reputation.

“We respect the decision of the Associated Press to no longer have its poll included in the BCS standings,” Weiberg said. “Since the inception of the BCS, the AP poll has been part of our standings. We appreciate the cooperation we have received from the organization in providing rankings on a weekly basis. We will discuss alternatives to the Associated Press poll at the upcoming BCS meetings and plan to conclude our evaluation of the BCS standings formula, including any other possible changes, by our April meeting.”

The AP said it had declined BCS overtures for any cooperative arrangements and that the BCS had access to the poll only from news outlets that published it, not directly from the AP.

Where the BCS goes from here won’t be determined for a while, but even before the AP made its poll off limits Weiberg had said that the BCS planned to look into the possibility of using a selection committee to create the bowl matchups, much like the NCAA Division I basketball tournament.

This season, the AP and coaches poll were given more weight than ever in the BCS standings. Each poll accounted for one-third of a team’s BCS grade and total points were factored in, not just ranking, which was the case before.

A compilation of six computer rankings made up the final third of teams’ BCS grade.

The new system put heighten scrutiny on the two polls.

In its letter, the AP said some of its poll voters had indicated they might no longer participate because of concerns over having their reporters be so closely involved in the process of determining which teams play where.

“By stating that the AP poll is one of the three components used by BCS to establish its rankings, BCS conveys the impression that AP condones or otherwise participates in the BCS system,” the letter said. “Furthermore, to the extent that the public does not fully understand the relationship between BCS and AP, any animosity toward BCS may get transferred to AP. And to the extent that the public has equated or comes to equate the AP poll with the BCS rankings, the independent reputation of the AP poll is lost.”

The latest BCS formula was installed after Southern California, the No. 1 team in both the media and coaches poll, was left out of the BCS title game last season. LSU beat Oklahoma for the BCS title, and USC won the AP title, creating the type of split championship situation that, in part, the BCS was created to avoid.

But the new system has also come under fire.

For the first time in the BCS era, three teams from major conferences — Southern California, Oklahoma and Auburn — finished unbeaten in the regular season. Auburn was left out of the Orange Bowl with the same 12-0 record that USC and Oklahoma had.

Texas passed California for the last at-large bid in the final BCS standings, and had many lamenting the BCS.

The ESPN/USA Today poll caught the brunt of the criticism in the Texas-Cal argument. Pac-10 commissioner Tom Hansen and Cal coach Jeff Tedford both called for the coaches to make their ballots public. That request was denied.

The AP votes are public information, and the final individual ballots were published the same day as the final BCS standings.

“The Associated Press has not at any time given permission to the Bowl Championship Series to use its proprietary ranking of college football teams,” the AP said in a statement Tuesday. “This unauthorized use of the AP poll has harmed AP’s reputation and interfered with AP’s agreements with AP poll voters. To preserve its reputation for honesty and integrity, the AP is asking the BCS to discontinue its unauthorized use of the AP poll as a component of BCS rankings.”