While first-quarter small-car sales lifted the U.S. average fuel economy of new light vehicles to a non “Cash for Clunkers” quarterly high, inventory shortages of some of the same models were the major force pulling down overall fuel economy in the year’s second quarter.

LVs sold between April and June averaged a 22.5 mpg (10.4 L/100 km, 2.4% better than year-ago’s 22 mpg (10.7 L/100 km). But that’s still a drop from the near-record Q1 Ward’s Fuel Economy Index rating of 22.7.

The decline in fuel economy came even as prices rose to $3.86 per gallon over the quarter, up more than a $0.50 from $3.32 in the first quarter.

The year’s first half saw the all-new Ford Focus propelled into the 15 top-selling-vehicles list in the second quarter and up to the No.6 spot in June, helping lift the overall Small Car market share.

However, deliveries of some of the most fuel-efficient small and midsize cars, including the Honda Civic and Toyota Corolla, plummeted as production stoppages caused by a March 11 earthquake and tsunami in Japan reduced inventory of those and other vehicles produced by Japanese auto makers.

As a result, both the Small Car and Middle Car segments saw their index rating drop even as their market shares rose.

Small cars accounted for 20.1% of second-quarter sales, the segment’s third-highest quarterly share since 1993, up nearly two share points from the year-ago. However, the segment’s index rating fell from 28 to 27.8, reducing the impact on the overall LV rating.

More significantly, the Middle Car segment, which accounted for 20.8% of second- quarter sales (up from 20.5% in the first quarter), saw its index rating fall a full point – from 26 to 25, as the Honda Accord and Toyota Camry, among others, were pushed to the sidelines due to depleted supply.

Related document: Ward’s Fuel Economy Index

The lack of Corollas and Camrys drove down Toyota’s average fuel economy to 24.9 mpg (9.4 L/100 km) from 26.2 mpg (9 L/100 km) in the prior quarter and knocked the perennial fuel-economy leader out of the top spot on the index, behind Nissan (25.3) and Kia (25.2).

Light-truck market share, which hit 50.6% in the first quarter, fell to 49.4%, while fuel-economy dipped slightly to 19.3 mpg (12.0 L/100 km). Cross Utility vehicles remained the best-selling segment in the market, despite a decline in share from 25.4% to 24.1%, which was accompanied by a slight drop on the index from 21.6 to 21.5.

The only segment to show any improvement in the second quarter was Vans, which saw its index rating inch up from 19.5 to 19.6 while taking a 2-year high share of 5.9%.

Domestic LVs retained their first-quarter rating of 21.8 on the latest FEI, up 1.6% over year-ago, with cars scoring 25 vs. a light-truck rating of 18.

Imported LVs rose 1% over year ago, despite a 1.4% quarter-to-quarter downturn equating to a 25.1 rating, with cars at 26.5 and light trucks at 22.