A KPMG report, leaked to the Northern Echo, revealed the figures included £750,000 of unsold merchandise.
Welcome to Yorkshire's Sir Gary Verity said the shortfall was outweighed by the "£102m economic benefit" to the region.
He said he regarded the loss as an "investment" in Yorkshire's economy.
Speaking after London turned down the chance to host the 2017 event, Mr Verity added he would "love" the race to return to the county by 2020.
It was too soon for Yorkshire to bid for the 2017 Grand Depart, Sir Gary said, but he was "very excited" by the prospect of it returning soon.
"The Tour de France, in its 112-year history, has never gone back to anywhere as quickly as that," he said.
"They do return to places but normally it's six, seven, eight or nine or 10 years...so three years would be way too fast."
Welcome to Yorkshire said it was back on track to deliver a "modest surplus" after the report by the accountancy firm last November revealed the losses.
Mr Verity said: "We had a loss that we made on it which we regard as an investment for the wider benefit of the Yorkshire economy, that's our job."
He added: "It was a multimillion-pound investment and we think that the payback from that for the wider benefit across Yorkshire will continue, not just from last summer to this summer, but for many years to come."
The tourism chief who helped bring the Tour de France to Yorkshire has defended the £1m loss his organisation incurred from hosting the event.