WASHINGTON — The Internal Revenue Service is making changes to its partnership with private companies that provide free tax preparation to millions of filers, following intense criticism of the program earlier this year.

The public-private partnership, called the Free File Alliance, was designed to provide free tax prep by a dozen private companies, such as H&R Block Inc. HRB, -0.09%   and Intuit Inc. INTU, -1.58%  , the maker of TurboTax, to about 100 million filers earning about $69,000 or less.

In recent years, however, fewer than three million filers used it each year, a sign the program wasn’t working well, taxpayer advocates and some lawmakers said. An outside review commissioned by the IRS found the program had serious flaws, but also provided substantial benefits.

Critics said some of the companies steered taxpayers away from Free File and into their paid commercial services. The IRS study, conducted by Mitre Corporation, a consulting firm that operates as an IRS research center, found that five of the 12 Free File partner companies used coding that in effect hid their Free File landing pages from many online searches.

The IRS said Monday its changes would make the program more accessible and enhance consumer protections.

An expanded version of this report appears on WSJ.com.

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