Madison’s highest paid city government employee last year wasn’t the mayor. It wasn’t the police chief. It wasn’t even the head of Metro Transit.

It was bus driver John E. Nelson.

Nelson earned $159,258 in 2009, including $109,892 in overtime and other pay.

He and his colleague, driver Greg Tatman, who earned $125,598, were among the city’s top 20 earners for 2009, city records show.

They’re among the seven bus drivers who made more than $100,000 last year thanks to a union contract that lets the most senior drivers who have the highest base salaries get first crack at overtime.

And there was a lot of overtime — $1.94 million last year, $467,200 more than the bus system budgeted for and the most ever for the system — as employees exhausted sick leave and took advantage of unpaid leave through the federal Family Medical Leave Act, officials said.

“That’s the (drivers’) contract,” said Transit and Parking Commission Chairman Gary Poulson. “(But) I think we want more information to the TPC and a discussion of all the facts.”

The high salaries for Metro bus drivers come as Metro’s ridership continues to grow and the system ranks high among peers according to a 2009 state audit. Metro, which increased fares last year, carried 13.58 million riders in 2009, the second highest total in 40 years.

Metro general manager Chuck Kamp, who earned $118,690 last year, defended the employees.

“These are very good employees who follow the rules that have been negotiated with the Teamsters,” Kamp said, adding that Nelson and Tatman “are senior drivers with excellent safety and customer service records.”

But he said Metro is looking at ways to limit overtime, including tighter follow up on workman’s compensation claims and exploring how to control the growth of Family Medical Leave Act time off by employees.

Nelson, Tatman and Gene Gowey, business manager for the bus drivers union, Teamster Local 695, could not be reached Friday.

In the past, drivers have defended the pay, saying they earn it by working long hours that can create hardships on families. Also, the job requires navigating an oversized vehicle through city streets and dealing with sometimes uncivil riders and other challenges, they have said.

The bus drivers’ contact, which calls for pay up to $26.02 an hour, expired at the end of December and the sides are now in negotiations.

Over all, Madison paid at least 20 employees more than $125,000 in 2009, according to city records.

After Nelson, the top paid employees in 2009 were City Comptroller Dean Brasser, who earned $151,551, and Police Chief Noble Wray, who made $143,585.

Mayor Dave Cieslewicz was paid $112,880. He wasn’t among the top 20.

Concern about bus drivers being among the city’s highest earners isn’t new. The issue surfaced after Metro changed from a Downtown hub to a transfer station system in 1998.

In 1997, before the change, no driver made more than $70,000. But two years later, as Metro struggled to fill vacancies, two drivers topped $100,000 and seven more made more than $70,000.

A high base salary and other benefits for drivers were largely set in the 1970s and 1980s, when the city took over the bus company.

Also, the union contract limits part-timers to 15 percent of the number full-time drivers, and part-timers can only drive morning and afternoon school routes. Those rules create opportunities for overtime and other special pay for full-time workers.

The city negotiated more flexibility for using part timers in 2002-03, but a state audit last year recommended Metro seek even more flexibility and noted that some pay premiums, such as those for evening and Sunday shifts, are uncommon in the industry.

In the past three years, Metro has been below budget for regular salaries, mainly due to vacancies, but exceeded budget for overtime, Metro data shows. In 2009, Metro was $290,000 under budget for salaries, spending $22.8 million, but $467,200 over budget for overtime, spending $1.94 million, the most ever.

Overtime is high for several reasons, Kamp said.

Metro employees are exhausting sick leave time, taking advantage of the federal Family Medical Leave Act and have high rate of absenteeism without pay, Kamp said.

For example, use of the medical leave act by Metro employees jumped 44 percent to 28,340 hours from 2008 to 2009, Kamp said, calling it “the driving factor” for overtime last year.

A city hiring freeze last year blocked Metro from replacing drivers for a time, Kamp said. Cieslewicz later authorized Metro to fill vacancies after learning it was cheaper than paying overtime.

Also, Metro undertook a safety program that took drivers off their jobs and increased overtime, Kamp said. But the training helped cut preventable accidents 17 percent last year, he said.

Metro is working with the Teamsters to control vacancies and absenteeism, including a progressive discipline system for absence without pay, Kamp said.

Already, Metro has cut worker’s compensation costs 27 percent to $632,600 between 2007 and 2009, he said.

Despite challenges with overtime, Metro’s cost per rider rose just 5 percent to $3.07 between 2006 and the third quarter of 2009, Kamp said.

“There are a number of things we’re trying to do to create efficiencies,” he said.