The government bank bailout is giving large institutions an unfair advantage, New York Times columnist Gretchen Morgenson writes in an opinion piece.

“It is perverse, of course, to reward big banks’ mistakes with bailouts financed by beleaguered taxpayers,” she says.

“But the too-big-to-fail doctrine benefits the banks in other ways as well: the implication that an institution will not be allowed to fall gives it significant cost advantages over smaller, perhaps more responsible competitors.”

She cites research from Dean Baker, co-director of the Center for Economic and Policy Research, to prove her point.

Using government data, he determined that the premium small banks pay for borrowing money over what big banks pay has risen markedly since Bear Stearns’ failure in March 2008.

That premium in favor of banks with at least $100 billion in assets registered 0.78 percentage point from late 2008 through June 2009, up from 0.29 percent in the fourth quarter of 2007.

And it’s the taxpayer that suffers in the end, Morgenson writes.

Baker determined that with the advantage of lower borrowing costs, 18 big banks received government assistance at a rate of $34.1 billion a year.

To be sure, the government’s aid helped stabilize the banking system amid the financial crisis. But many experts say the big banks have merely papered over their woes.

“When the government stops buying assets, who steps in?” Meredith Whitney told CNBC.

“Core earnings of these banks still aren’t what people expect.”