Chevron, the second-largest U.S. oil company, warned on Wednesday that third-quarter earnings would be lower than in the second quarter due to "significantly lower" earnings from its refining division as fuel margins were squeezed.

The company also said second-quarter earnings included foreign exchange gains of about $300 million, whereas it anticipated similarly sized losses for the third quarter.

Chevron shares fell as much as 1.2 percent in after-hours trading, extending a small decline during the regular session.

Analysts, on average, had been expecting earnings per share of $3.08 for the third quarter, which would have been up from $2.77 in the second quarter and $2.57 in the third quarter of 2012, according to estimates on Thomson Reuters I/B/E/S.

In its interim update for the third quarter, Chevron said crude-input volumes at its U.S. refineries were slightly higher as its Richmond, California, plant resumed normal operations following an August 2012 fire, offset by planned maintenance at its El Segundo refinery to the south.

International crude-input volumes rose from the previous quarter, but the company also cited a handful of industry figures showing margins for its fuel heading lower.

Oil and gas production from wells rose slightly from a depressed second-quarter level, with maintenance in the Gulf of Mexico curbing overall output. Oil and gas production accounts for about nine-tenths of the company's business.

Average U.S. oil-equivalent production of oil and gas fell to 651,000 barrels per day in July and August from an average of 659,000 for the entire second quarter.

Worldwide, Chevron produced 2.59 million bpd in the first two months of the third quarter, up from 2.58 million in the second, with output outside the United States picking up as production projects resumed.

The company reports full third-quarter results on Nov. 1.