Fannie Mae and Freddie Mac have again reported profits, though at levels much lower than a year earlier, as their regulator continues to prepare for what could be several more years of uncertainty about the companies' future.

Based on the latest earnings reports, the companies by June will send combined dividends of about $2.5 billion to the U.S. Treasury, bringing their total payments to the government to more than $230 billion.

Fannie Mae on Thursday reported net income for the first quarter of $1.9 billion, down from $5.3 billion in the same quarter last year. Freddie on Tuesday reported net profit of $524 million, compared with $4 billion in the same quarter last year.

Both companies' earnings were affected by accounting quirks driven by how the companies value some derivatives, and didn't benefit as much from some one-time items, such as settlements and gains related to rising home prices.

FTN Financial analyst Jim Vogel wrote in a note to clients that Fannie "remains on a sustainable business model, just not one profitable enough to support any reasonable level of capital."

Fannie and Freddie don't make loans. They buy them from lenders, wrap them into securities and make guarantees to make investors whole if the loans default. After suffering heavy losses in the wake of the housing bust several years ago, the companies were taken over by the government and put into a conservatorship under the Federal Housing Finance Agency.

A bipartisan bill that would have replaced Fannie and Freddie with a new system fell through a year ago, and since then lawmakers have shown little interest in a renewed push.

Under an agreement that provides the companies with their government backstop, the companies since 2012 have sent nearly all their profits to the Treasury, though some shareholders are challenging that arrangement in court.

As part of that agreement, both Fannie and Freddie have also significantly wound down portfolios of mortgages invested in during the housing boom. On Thursday, Fannie said that fees from its core business of guaranteeing mortgages represented the majority of its revenues, a trend that CEO Timothy J. Mayopoulos said he expects would continue.

The agreement also requires the companies to reduce their capital buffers each year, eventually reaching zero in 2018. A stress test released in April said that the companies would need up to $157.3 billion in support from the government in a severe economic downturn.

A survey of senior loan officers released by the Federal Reserve this week said most banks didn't expect mortgage access to ease in response to efforts that Fannie and Freddie have made to limit penalties for making mistakes on loans. Mr. Mayopoulos said Thursday he believes some lenders have lifted some restrictions but that the process would be gradual.

Both Freddie and Fannie have done robust business in financing rental housing this year, and on Thursday the FHFA announced that it would change how it limits that line of business. The companies are forbidden from doing more than $30 billion in new multifamily lending this year, a limit that they were on pace to barrel through sometime in the latter half of 2015.

Rather than raise the $30 billion caps, the FHFA said it would broaden the categories of loans that are excluded from the caps, a move that FHFA Director Mel Watt said is meant to support affordable rental housing.

On Tuesday, the FHFA said it authorized the companies' boards to review the compensation packages of Mr. Mayopoulos and Freddie CEO Donald Layton, and possibly propose higher pay for the executives in part to help retain them and make it easier to find successors should one of them leave. Both CEOs receive salaries of $600,000, which are capped. The decision by FHFA has already received significant blowback from the White House, as well as some lawmakers from both parties.

On a call with reporters on Thursday, Mr. Mayopoulos declined to comment on the decision, but said, "I don't have any plans to go anywhere. I'm enjoying my role here at Fannie Mae and am honored to lead this organization at this moment in time."

Write to Joe Light at joe.light@wsj.com

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