Officials at First Niagara Financial Group, which earlier this year acquired New Haven-based NewAlliance Bancshares, said Thursday the merger went smoothly but resulted in significant expenses that impacted First Niagara’s second-quarter earnings.

Buffalo, N.Y.-based First Niagara said its net income last quarter was $13.6 million, compared with $20 million in the second quarter of 2010.

Those figures represent GAAP earnings, meaning they conform to Generally Accepted Accounting Principals — an industry standard that is the commonly accepted way of reporting earnings.

Bank officials noted the second quarters of both 2010 and this year “reflect significant acquisition, integration and restructuring expenses.” First Niagara completed its acquisition of NewAlliance in April.

The NewAlliance deal was the company’s largest merger to date, First Niagara Chief Financial Officer Gregory Norwood said in a conference call with investors.

Even with those expenses, however, bank officials said the second quarter was an encouraging one.

“It’s another solid quarter,” President and CEO John Koelmel said in the call with investors.

“While our New England team successfully completed the NewAlliance conversion, seamlessly converting 350,000 customer accounts in Connecticut and Massachusetts, our continuing focus on our customers and all of the markets we serve again resulted in very strong loan and deposit growth,” President and CEO John Koelmel said.

As of June 30, First Niagara had about $31 billion in assets and $19 billion in deposits. The company, through its wholly owned subsidiary First Niagara Bank, has 346 branches and about 5,000 employees in Connecticut, upstate New York, Pennsylvania and Massachusetts.

Like most financial companies, First Niagara also reported non-GAAP earnings. Companies report these earnings in addition to the required GAAP ones because they often feel non-GAAP figures more accurately reflect a business’ performance by eliminating non-recurring factors.

On a non-GAAP basis, First Niagara’s earnings — which the company calls “operating earnings” — totaled $71.2 million last quarter, up from $44.9 million a year earlier. Those figures, however, do not take merger expenses and various other factors into account.