A U.S. judge in Minneapolis denied a request from small banks and credit unions to block part of Target Corp.'s recent $19 million settlement with MasterCard Inc. over its 2013 data breach, but acknowledged that terms of the pact "do not appear altogether fair or reasonable."

In a four-page ruling handed down late Thursday, U.S. Judge Paul Magnuson said that there wasn't any indication that MasterCard is misleading or coercing banks and credit unions into accepting terms of the settlement.

"Although the settlement may not "pass the smell test," as the saying goes, it is not serious misconduct," the judge wrote in his decision.

Representatives of Minneapolis-based Target and Purchase, N.Y.-based MasterCard said they were pleased with the judge's decision.

"Each impacted bank and credit union will review the terms and make an independent decision on whether to accept the settlement," a MasterCard spokesman said.

Target's data breach in late 2013 compromised 40 million credit- and debit-card accounts. A group of small banks and credit unions had asked the court to allow them to pursue additional compensation for losses that they incurred as a result of the breach. The $19 million settlement, announced last month, includes a traditional provision that prohibits banks that participate in the pact to seek other reimbursement claims. Small banks were hoping to block part of the deal in an effort to remove that provision.

The banks say that they are only reimbursed pennies on the dollar in such cases and should be allowed to pursue compensation in other ways.

Lawyers representing the small institutions said the judge's ruling "should give financial institutions great pause before accepting this flawed and inadequate agreement."

The lenders' request came as part of their lawsuit against Target. MasterCard isn't officially a party to the case. MasterCard initially sought more than $26 million from Target, according to the judge's ruling.

The judge also noted that the court's authority over the settlement is limited because the case hasn't been certified as a class-action lawsuit. The plaintiffs are seeking class-action status.

Paul Ziobro contributed to this article.

Write to Robin Sidel at robin.sidel@wsj.com

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