Greg McBride, Bankrate.com's chief financial analyst, told CU Times that short-term interest rates will likely rise in the middle of next year while long-term interest rates could rise at any time.

"As we saw this time last year, that can happen very suddenly. We've been lucky so far in 2014 in that long-term rates have actually moved down – not to say that's going to continue in perpetuity as we get closer to an eventual hike in short term rates by the Fed," McBride said.

"Long-term rates can move up at any point. Some of the inflation indicators of late are the type of thing that could make investors nervous and push long-term rates higher," he said.

McBride said the NCUA's interest rate concerns are valid. He predicted that a long-term rate hike could occur well ahead of any short-term rate increase by the Fed.

"We got a snapshot of that last year where long-term interest rates jumped a full percentage point in about a seven-week period and as a result, a lot of bond funds suffered losses for 2013. It was a harsh reminder of interest rate risk and that's the type of thing that could certainly happen again," he said.

Credit union executives who asked to remain anonymous said the $1 billion First Financial Federal Credit Union in Lutherville, Md., and the $394 million Erie Federal Credit Union in Erie, Pa. have sold off long-term investments at a loss due to the NCUA's interest rate fears.

According to First Financial's latest call report, the credit union reported a non-operating expense of $4,691,000 as of March 2014. That same period, Erie reported a non-operating expense of $3,682,009. First Financial's resulting net loss was $2,421,606, while Erie reported a $3,253,371 net loss.

As of March 2014, Erie's supervisory interest rate risk threshold was 318.52 and First Financial's was 244.12.

First Financial and Erie did not return multiple requests for comment.

While APCO has not been required by the NCUA to make any changes due to interest rate risk, Mann said APCO has to win under any interest rate scenario.

"We've got to win if interest rates go up. We've got to win if interest rates go down. We've got to win if interest rates stay the same. We can't bank on interest rates going up, and that's what the NCUA is asking us to do – to bet on interest rates going up, and they've been wrong for the past six years," Mann said.

"That's a little bit concerning to us. We've got to continue to make money and provide value. We're not extending risk or anything like that," he said.

Mann said CUNA presented APCO with the 2013 member benefits top performance award at the GAC for delivering more benefits to members than any credit union in the nation.

"The article did have a little bit of a blindside because we did have a good discussion for 30 to 40 minutes, but he picked out one or two sentences that would fit the agenda to support the story that credit unions are piling in long-term risk in investments, and that's actually incorrect for us," Mann said.

CFO Blane Mink said he is not sure if the NCUA suggested the WSJ contact APCO, or if the reporter decided to contact the credit union on his own.

"I told Mr. Mann the reporter had insisted too many times that no one at the NCUA had told him to call us. He mentioned that three or four times. That concerned me because he said it over and over. He was protesting too much," he said.

NCUA Public Affairs Specialist John Fairbanks said no one at the NCUA pitched WSJ on the story or suggested any interview subjects.

NCUA Board Chairman Debbie Matz was quoted in the original WSJ article as saying she is concerned the agency's message on interest rate risk is not getting through, or credit unions are listening but choosing not to do anything about the issue.

In the same article, Mann said the credit union would likely hold on to its long-term investments instead of selling them at a loss.

"You can't avoid risk," he said. "We do try our best to mitigate risk in the best possible way.

Mink explained that the credit union had significantly shortened the duration and maturity of its investments. Mink said WSJ sent him an extremely complicated spreadsheet of data sourced for their story. Mink added that the article ran before he could examine what the reporter was using as his evidence.

"I was a little surprised by the headline of the article. It told us how the article was going to be tainted and biased and then certainly pulling one sentence out of a 40-minute conversation and then indicating that this credit union was piling into long-term investments was not fair," Mink said.