The parliamentary budget officer's latest analysis of the government's spending estimates shows the Crown corporation will cost the public purse an additional $236 million this year, bringing the total to $362 million for 2013-14.
The additional money is for AECL's research and development program.
The federal budget watchdog says although Ottawa's support for the troubled nuclear agency has decreased by 60 per cent over the last four years, the booked savings in terms of direct support for operations is misleading.
At the same time, AECL's losses have ballooned: from $300 million in 2009-10 to $3 billion over the first three quarters of 2012-13.
"As a wholly-owned Crown corporation, the government of Canada is ultimately responsible for AECL's liabilities," the PBO points out.
Overall, the report calculates that the government will spend $1.1 billion more during the current fiscal year than what was contained in the main estimates issued in early March. That will bring spending for the 2013-14 fiscal year to about $253.6 billion.
Other adjustments include increases to transfer payments and subsidies to Crown corporations, including a $99,000 top-up to cover Via Rail's pension plan deficit.
The report notes that even with the increases, the spending plans for the current fiscal year are $5.4 billion lower than last year, due to government austerity measures introduced in 2012.
The findings suggest that Finance Minister Jim Flaherty is largely meeting his targets for spending, which the government predicts will result in a balanced budget for the 2015-16 fiscal year.
"As noted in earlier PBO analysis, virtually all of this decrease (in spending) stems from the fiscal strategy to balance the budget through constraining direct program spending, in particularly operating spending by departments and agencies," the report concludes.