Even as stock market rose last year, pension funding levels at America's biggest companies in 2014 fell to levels not seen since just after the financial crisis.

One big reason: Employers cut back on contributions to their plans to the lowest amount in six years, according to an analysis by benefits consultant Towers Watson, thanks, in part, to a break offered up by Congress last summer to bail out the Highway Trust Fund. (Tweet This)

As employers cut back on contributions, pension plans face higher costs meeting their financial promises to retirees. Last fall, new mortality tables showing retirees are expected to live longer raised pension plans' liabilities, forcing them to set aside more money to meet them.

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Pension plans also face the ongoing drag of lower interest rates, according to Alan Glickstein, a senior retirement consultant at Towers Watson

"We're seeing some pretty good investment returns over the past few years but there being more than offset by liabilities being driven up by lower rates," he said.

Low interest rates hurt pension funds two ways. First, they lower the returns on safe, fixed income investments like Treasury bonds. But they also drive up the current cost of providing a fixed monthly payment to retirees well into the future. That means companies have to set aside more money in their pension plans to cover the increased liability created by lower rates.

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But many companies argue that the current era of record low interest rates is an anomaly—and that rising rates will eventually make up for the shortfall created, in part, by the ultra-low rates engineered by the Federal Reserve to repair the damage to the financial system after the 2008 collapse.

"If you believe that interest rates will be higher not too many moons down the road here, and that to some extent they're being pushed down by government policies to stimulate the economy, you wouldn't view current rates as the most realistic funding target," said Glickstein.

That's one reason Congress last summer gave companies a break on their pension fund contributions, allowing them to "smooth" the way they account for the ups and downs of interest rates over a longer period. That allowed them to cut back on pension fund contributions by as much as $50 billion, according to one estimate by Moody's.