Polls opened late, election workers had problems starting up new touchscreen voting machines and others had troubles with ballots that wouldn't scan.
Bush's action came at the urging of Secretary of State Jim Smith. Janet Reno, who hopes to challenge Bush in November earlier sought a court order to extend polling only in counties that reported trouble.
Polls will now close at 9 p.m., meaning voting will not end until 10 p.m. Eastern time because parts of the Panhandle are in the Central Time Zone.
The state changed voting laws and outlawed punchcard ballots after the 2000 presidential election debacle. Tuesday's primary was the first statewide test of an election system touted as a model for the nation.
But problems were reported from Miami to Jacksonville. In one precinct in a predominantly black Miami neighborhood, voting didn't begin until 11:45 a.m., nearly five hours after polls opened. Officials estimated about 500 people left the precinct without voting.
"Nobody has been able to vote in this district, period," said Delbra Lewis, who attempted to vote three times by late morning. "I've been here since 7 a.m. and I haven't been able to vote."
A precinct at a senior center near downtown Jacksonville opened 90 minutes late because poll workers didn't realize they were supposed to turn on machines themselves. Dozens of voters left without casting ballots.
Election workers in Orlando said 42 percent of Orange County's ballots would have to be counted by hand after polls closed. The ballots were tearing as they were fed through optical scanning machines, making them unreadable. The county has nearly 426,000 voters.
In Miami, Reno was delayed from voting after arriving first at her precinct when election workers struggled to get new touchscreen machines up and running.
The former U.S. attorney general and others waited several minutes while an election official booted up one of the 18 machines. Some gave up and left, exasperated with the delay.
"Any time you have a new system, you're going to have problems. We expected problems, but not to this magnitude," said Gisela Salas, Miami-Dade's assistant supervisor of elections.
State election law requires that polls open at 7 a.m., but doesn't say anything specific about what happens if they don't.
In Broward, which has more registered voters than any of Florida's 67 counties, some precincts didn't open on time at 7 a.m. because poll workers didn't show up and one opened nearly two hours late because workers didn't have the right equipment.
In Boca Raton, where two candidates sued over Palm Beach County's new voting machines, Ellen Siegel left her polling place without casting a ballot.
Siegel said she and several other voters were given the plastic cards they needed to insert into the new ATM-style voting machines, but they read "invalid."
"No one had any idea how to get the machines up and running. I didn't get to vote and there are going to be a lot of other people who won't be able to do it," said Siegel, a 15-year resident of the city.
Still, Palm Beach County elections chief Theresa LePore said she's faced few problems. Some poll workers didn't show up, so some polls have minimal staffing levels, but all opened on time.
"So far, so good," she said.
Officials in other large counties also reported few problems, including Hillsborough and Pinellas in the Tampa Bay area.
But in Miami, at a polling place in the southwest suburbs, about 100 voters were in line when the polls opened, but only five of 20 machines were functioning 30 minutes later.
"You'd think that after 2000, it'd be working," voter Betty Lanese said during her 50-minute wait to vote. "I would have expected some problems from the voters themselves, not from the elections department."
State elections officials initially dismissed many of the problems as common and said much of the commotion results from the national spotlight shining on Florida after the state held the 2000 presidential election in limbo for 36 days.
Florida spent $32 million to reform its election system and more than half of the state's voters will use new touchscreen voting machines, as opposed to the punchcard and butterfly ballots that were the focus of the 2000 election. The computers are designed to simplify the once-muddled elections process.
Reno eventually voted without any other problems after election officials managed to start up the new machines one by one, each taking at least six minutes to get running.
"I think that it is important that the voters overcome mistakes made by others or failure to plan by others," she said.
Reno is facing Tampa lawyer Bill McBride and Miami Sen. Daryl Jones in the Democratic gubernatorial primary.
Besides the Florida contest, there are races in New Hampshire, Arizona, Connecticut, Georgia, Maryland, Minnesota, New York, North Carolina, Rhode Island, Vermont, Wisconsin and the District of Columbia.
In New Hampshire, two-term GOP Sen. Bob Smith is in danger of being ousted by Rep. John E. Sununu, who was recruited by state Republicans.
Smith left the party in 1999 for an ill-fated presidential run, accusing the GOP of hypocrisy and saying the party platform was "not worth the paper it's written on." After losing badly in his home state primary, he rejoined the party a few months later.
In the past 20 years, only one elected senator has been ousted in a primary: Illinois Democrat Alan Dixon lost in 1992 to Carol Moseley Braun, who went on to serve one term as the nation's first black female senator.
In North Carolina, the Senate seat held for 30 years by retiring Republican Jesse Helms drew crowded primaries, with Dole leading seven candidates for the GOP nomination and former Clinton White House chief of staff Erskine Bowles among nine Democrats.
Open governor's seats also spurred competitive and often high-spending contests in Arizona, New Hampshire, Rhode Island and Wisconsin.
The New York governor's race simmered down last week when Andrew Cuomo dropped out of the Democratic primary, clearing the way for state Comptroller H. Carl McCall to take on Republican Gov. George Pataki this fall.
In Washington, D.C., Mayor Anthony Williams was dropped from the Democratic primary ballot because of petition irregularities. He is running as a write-in candidate, as is his chief opponent, the Rev. Willie Wilson. In Providence, R.I., four Democrats are vying for the nomination to replace ousted Mayor Vincent "Buddy" Cianci Jr., who was sentenced to prison last week for corruption.
Several House seats also drew attention, including former Florida Secretary of State Harris' bid for a safely GOP House seat, and Kennedy cousin Mark Shriver's run for the Democratic nomination to challenge eight-term GOP Rep. Constance Morella in Maryland.