As consumers take advantage of low interest rates to refinance their mortgages, banks and other investors are getting hit by high levels of prepayments that reduce the long-term value of their mortgage-backed investments.

That is what’s happening to First Niagara Financial Group, which said Wednesday that it will take a pretax charge for the fourth quarter of $16 million, or 3 cents per share, because the mortgage investments in its securities portfolio are being paid off faster than expected.

That means it can’t count on a stream of earnings from the loans over a long period of time, so it has to write down the value of the investments because they won’t last as long as originally assumed.

The Buffalo-based bank said it’s speeding up the amortization – the gradual accounting for changes in value – of premiums on its collateralized mortgage obligations, or CMOs. These are collections of other securities that are ultimately backed by consumer mortgages.

The action by the bank reflects the “substantial level of prepayments” on the mortgages in recent months and “the expected elevated levels of cash flows to be received for the foreseeable future.”

The bank’s portfolio of residential mortgage securities totals $5.7 billion, including $4.8 billion of CMOs and $800 million of traditional mortgage-backed securities. The remaining unamortized premium on that portfolio is $96 million, with $74 million on the CMOs.

Nevertheless, the bank said, it still expects to report operating earnings per share in line with Wall Street analysts’ current projections of about 18 cents per share.

First Niagara, with 430 branches and $37 billion in assets in four states, said that it would report earnings Jan. 23.