There has been a 23 per cent reduction in funding since 2006, Trudeau said during question period in the House of Commons Tuesday.
The Liberals say the government budgeted $10 million for the Public Health Agency of Canada's immunization program in the 2006-07 fiscal year, compared to $7.7 million for the year ending March 31, 2015.
"There are five new measles cases in Ontario. The prime minister has run no ads promoting the life-saving benefits of vaccinations," Trudeau said.
"Will he stop his self-promoting partisan government ads and invest instead now in a campaign that encourages parents to vaccinate their kids?"
Prime Minister Stephen Harper didn't say whether the government was planning ads promoting vaccination, noting simply that he sees promoting its programs as one of the government's responsibilities.
"The minister of health and other members of the government have been very clear on the fact that Canadians should seek proper vaccines against measles and against a range of other illnesses," Harper said.
"These vaccines have historically proven extremely effective in reducing and in some cases even eliminating certain types of previously debilitating ailments."
The numbers provided by the Liberals are recorded in the agency's annual reports on plans and priorities and departmental performance reports.
But the performance reports show the agency's spending on the immunization program was about the same in 2006-07 as it was in 2013-14.
The actual spending in the fiscal year that ended March 31, 2007 was $8.6 million. Similarly, the amount spent on the immunization program in 2013-14 was $8.4 million.
There are several years in the middle in which it's difficult to compare the numbers because the immunization program spending wasn't separated from the overall infectious disease prevention and control program.
Last week, Health Minister Rona Ambrose urged parents to have their children vaccinated, saying the anti-vaccine movement puts people at risk.
It's up to the provinces and territories to fund vaccinations, but the federal program aims to encourage "maximum vaccine uptake and coverage, [provide] information on vaccine surveillance and safety, and [ensure] a safe and affordable supply of vaccines" under the National Immunization Strategy, according to the Public Health Agency's 2014-15 report on plans and priorities.
A 2012 audit found the immunization program lacked a strategic plan and that the agency hadn't clearly communicated its role or mandate to its partners.
The audit also suggested the Centre for Immunization and Respiratory Infectious Diseases, which oversees the program, was overstaffed.
"We found limited evidence that centre management has sufficient information on required levels of effort for the centre’s activities to validate the human resource estimates allocated to them. To that end, we noted that the centre has recently begun an analysis to better understand workloads and their impacts on human resource requirements for certain immunization program activities," the audit said.