(FORTUNE Magazine) – What's so strange about the battles over the economic stimulus legislation is that President Bush has been largely absent from them. Yes, we know there's a war in Afghanistan and an anthrax scare at home, but that isn't the whole story.

Unlike the President's national security team, which has proven to be stocked with pros, Bush's economic squad has blundered along for months. One result has been a legislative process fraught with delays and some of the ugliest partisan squabbling since the Sept. 11 attacks. Any hope that tax rebates might reach consumers in time for the holiday shopping season has been dashed in part by the lack of firm White House guidance.

When Bush assembled his economic team last year, Washington expected discipline to be meted out by two people: Larry Lindsey, the White House's chief economic advisor, and Treasury Secretary Paul O'Neill. But neither has emerged as a credible force on Capitol Hill. Some White House aides have even groused privately that Lindsey and O'Neill lack the political skills necessary to negotiate anything as high-stakes and sensitive as a major tax bill.

Lindsey has never functioned as much more than a policy wonk. Coordination of fiscal initiatives in the West Wing has fallen instead to Deputy Chief of Staff Josh Bolton. A former investment banker at Goldman Sachs, Bolton heads something called the Domestic Consequences Principals Committee, which watches over all non-foreign affairs policymaking. Lindsey makes suggestions there and, to the chagrin of some of his colleagues, has dabbled in congressional mediation. But he's treated by lawmakers as staff and is sometimes ignored at the White House too.

O'Neill has worse problems. The Treasury chief has made so many public gaffes--including labeling a House Ways and Means Committee drafting session "show business"--that a growing number of Republican lawmakers have called for his resignation. Ways and Means Chairman Bill Thomas and the Senate's Republican leaders have taken turns upbraiding him for his loosely phrased criticisms of GOP actions. "Do you understand the consequences of what you said?" Thomas once asked O'Neill. As a result, O'Neill has spent a lot of his time apologizing to members of Congress rather than representing the President. Complicating matters further, O'Neill, a moderate, and Lindsey, a conservative, have long clashed over policy and procedure.

For the moment it's not entirely clear who's in charge. Lately Bush has stepped up himself, insisting on quick action on the stimulus plan as well as some spending restraint. Congress will probably comply before it recesses next month. But getting there has exposed the Administration's weakest link.