The troubled Pan Am Games have a new coach just 19 months from the starting line.

Chief executive officer Ian Troop, who was paid $390,000 a year to helm the 2015 sports extravaganza, was unexpectedly fired Friday over what sources told the Star were “leadership issues.”

Troop will be replaced as of Jan. 6 by deputy Health Minister Saad Rafi, who earned $428,000 last year for running the largest provincial department with a $49-billion budget.

“There is no malice here. These things are never easy. The question is who’s the best guy for the circumstances,” said Toronto 2015 Pan Am/Parapan Am Games Organizing Committee chair David Peterson, the former Liberal premier.

“This kind of thing happens in most of the multi-sport games. They are enormously complicated things and they have different phases to them and different skills are required,” said Peterson, who insisted the Games, which open July 10, 2015, are “in very good shape.”

“They’re just a million moving pieces, there are just so many things that can go wrong . . . and Saad is just a brilliant guy at running very complicated properties.”

It will cost taxpayers at least $2.5 billion to host the Games, which will host 7,666 athletes competing in 51 sports at venues in 14 municipalities, including Toronto, Hamilton, Milton, Ajax, Whitby, Oshawa, Caledon, St. Catharines, and Welland.

Rafi, who will receive the same salary he made at Queen’s Park, said Peterson approached him “a few days ago” with the job.

“I’m going to have to get up to speed very, very quickly,” he said, adding the Games’ biggest challenges are “obviously security, transportation and logistics.”

Tourism, Culture and Sport Minister Michael Chan stressed it was the Pan Am board’s decision to sack Troop.

“I’m happy with Rafi because of his proven record. He’s able to consult with different government ministries,” said Chan.

Troop, who is expected to get a year’s salary in severance, had been under fire over his expenses, which were causing a political headache for Premier Kathleen Wynne’s minority Liberal government.

Peterson played down the controversy over the “peanuts” expenses that Troop and other senior executives were charging.

“It didn’t violate any policies. It looked bad. That was not the issue (in his firing). That had nothing to do with it,” he said.

However, two sources said the well-liked Troop, who did not return a call from the Star, confirmed there were “leadership issues.”

Indeed, a kerfuffle over free Cadillacs offered to senior officials by General Motors Canada, a Pan Am sponsor, was an early indicator of problems.

Some Games executives practically rebelled when an “upset” Troop told them they could not accept the luxury automobiles and were forced to settle for sharing a pool of Chevrolets.

“It reflected badly on him,” said one Pan Am insider, stressing the ousted CEO understood the poor optics of Games brass driving around in Cadillacs but struggled to convince his executive team of that.

Progressive Conservative MPP Rod Jackson (Barrie), a vocal critic of the Games, said things “started to go sideways” under Troop’s watch, “but I am not sure that a career bureaucrat is the right choice” to replace him.

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The Games have been plagued by expense concerns starting in October, ranging from generous moving allowances and niggling parking expenses to 200-per-cent bonuses for senior staff if the event comes in under budget.

In Troop’s case, he would have been eligible for a $780,000 payout.

“It is interesting that the new skipper is the same guy who was involved in the ORNGE scandal,” said Jackson, referring to Rafi’s tenure at the health ministry when the scandal at the air ambulance service erupted. Ontario Provincial Police are still investigating ORNGE.

Paul Henderson, former International Olympic Committee member and Toronto 1996 Olympic Games bid chief, said Troop had an impossible job trying to put together the largest sporting event in Canadian history with a budget of $1.44 billion.

That tally excludes the $709 million for a Games village at the West Don Lands, $206 million for security, and $75 million to $90 million for transportation.

“The (Pan Am) bid book was written for political reasons, not on how one runs the Games or the sustainable legacy after. He tried to deliver what he was hired to do, but it was, and is a, daunting task,” said Henderson.

NDP MPP Paul Miller (Hamilton—Stoney Creek) said the Liberals are desperate to sweep Pan Am controversies under the rug.

“The government’s scrambling to throw Mr. Troop under the bus after defending his sky-high salary and severance for months,” said Miller.

Peterson conceded the Games are under an “enormous amount of scrutiny.”

“Every coffee and every parking ticket is being scrutinized . . . we (the Games) have become a stick to beat the government with,” he said, emphasizing the good news is “that we are way under budget.”

In fact, Peterson said the biggest hurdle facing the Games is building interest in the event among all Ontario residents.

“That is our biggest challenge going forward for the next year and a half,” he said.