The 71-year-old veteran of Illinois politics was still en route from his home state when Majority Leader Harry Reid announced he would not be permitted to take his seat when other new lawmakers are sworn into office. Burris "has not been certified by the state of Illinois" Reid said, a reference to incomplete paperwork that barely begins to describe the dispute.
While Burris has not been accused of any wrongdoing, he was named to the Senate last week by Illinois Gov. Rod Blagojevich, who faces charges of having attempted to sell the seat.
Senate officials said it was possible Reid would try and have Burris' case referred to the Rules Committee for review, a move that would effectively sidetrack the issue while the complicated political and legal situation in Illinois could be sorted out. They spoke on condition of anonymity, saying they were not authorized to discuss possible developments.
Reid, D-Nev., had appeared to leave open the possibility of a compromise over the weekend after failing to persuade Blagojevich to leave the seat vacant. Burris is to meet privately on Wednesday with the majority leader in his office a few paces off the Senate floor.
Burris, who is black, downplayed the issue of race at a news conference before boarding a flight from Chicago to Washington - even though supporters have given it prominence.
"I cannot control my supporters. I have never in my life, in all my years of being elected to office, thought anything about race," he said.
He said repeatedly during the day that he is a senator, but in fact he is not and cannot be unless he is administered the oath of office.
Other controversy aside, Democrats privately expressed concern that Burris would not be able to hold the seat in a special election that must be held in 2010. Reid has denied that political calculations are involved, but one Democratic official suggested that one potential outcome would be for Burris to be seated and pledge to retire in 2010.
Burris sidestepped the issue at an airport news conference before leaving Illinois, saying, "I can't negotiate in the press."
The Illinois seat was one of two in dispute on the eve of the ceremonial opening of the new Congress.
In Minnesota, the state Canvassing Board certified results showing Democrat Al Franken winning a recount over Republican Sen. Norm Coleman, but a legal challenge probably will keep that race in limbo for now.
Reid called Franken the winner - in a claim that Republican National Committee chairman Mike Duncan swiftly rejected.
Despite losing several seats last November, Senate Republicans have the ability to block any quick attempt by Democrats to allow Franken to be sworn in, and it was not clear whether Reid intended to press the matter on Tuesday. Coleman's term has expired, meaning Minnesota, like Illinois, could be represented by only one senator for an undetermined period.
Reid and Senate Republican Leader Mitch McConnell of Kentucky arranged an early evening meeting to discuss the two seats.
The uncertain Illinois script played out as a federal judge granted prosecutors more time to seek a formal indictment of Blagojevich, and state lawmakers marched methodically toward impeachment proceedings that could result in his removal from office. He was arrested last year and charged with trying to sell Obama's seat.
Blagojevich appointed Burris to fill take Obama's former Senate seat last week, defying the wishes of Senate Democrats who had warned that anyone he named would be tainted by association. His selection of the 71-year-old former officeholder instantly exposed rifts among Democrats, evident at a send-off Burris received in a Chicago church on Sunday night.
Rep. Bobby Rush, D-Ill., called the Senate "last bastion of plantation politics," and said blacks had been "excluded systematically for too long."
There were mounting legal complications, as well.
While Blagojevich has signed formal appointments papers, Jesse White, the Illinois secretary of state, has not, and Senate rules require that signature.
Burris, in turn, has gone to court hoping to win an order for White to sign the necessary paperwork, and has also threatened to sue to take his seat in the Senate.