Paychex serves small- and medium-sized businesses, which have recovered from the recession more slowly than large corporations. The company said growth in its "checks per client," the number of paychecks clients issued during the quarter divided by its average customer base, slowed to 1.5 percent from 2 percent growth in the June-August quarter.

The company said it expects a "moderation" in the measure, a barometer of the health of smaller businesses, over the next six months because of the slow economy.

Net income in the period ended Nov. 30 rose to $140.4 million, or 39 cents per share, from $133.9 million, or 37 cents per share, in the same months last year. Revenue increased 7 percent to $545.7 million from $512 million.

Analysts polled by FactSet had expected earnings of 38 cents per share on revenue of $551 million.

During the September-November quarter, net income increased thanks to the bump in checks per client, Paychex's price increases and lower discounting in the client base. The company's smaller HR services division also helped results as it added clients and existing clients' employees rose.

The quarter got a boost from two companies acquired earlier in 2011.

The Rochester, N.Y., company backed its previous guidance of 5 to 7 percent growth in net income for the year ending in May 2012. That suggests net income of about $540 million to 550 million, which brackets analysts' estimates.

Shares dropped 6 cents to $30.18 in after-hours trading. The stock had closed up 64 cents at $30.24 during the day's trading.