Prices were down 1.1% compared with the same quarter in 2011.
London saw the strongest quarterly growth rate, with prices up 1% quarter-on-quarter.
While the annual rate of growth slowed a little from 2.3% to 1.2% average prices in the capital have now virtually recovered to their 2007 peak.
Robert Gardner, Nationwide's chief economist, said: "The north/south divide amongst the English regions continued in Q2, with house price growth in southern England (South West, Outer South East, Outer Metropolitan, London and East Anglia) exceeding that of northern England (West Midlands, East Midlands, Yorkshire & Humberside, North West and North) for the thirtieth consecutive quarter.
“The North West was the worst performing English region, with prices down 4.1% year-on-year.
"Scotland was the worst performing area on a quarterly basis, with prices falling 2% during the second quarter. This pushed the annual rate of change down to -2.3%.
"Wales saw a third successive quarter of price falls, with a seasonally adjusted fall of 1.1% in Q2. On an annual basis, prices were down 5.3% compared with 2011.
"Northern Ireland continued to see price falls, with average prices down 10.6% year-on-year.”
Research house Capital Economics said on its own, the latest modest drop in the Nationwide house price index was not "hugely significant".
Ed Stansfield, chief property economist at Capital Economics, added: "But since the turn of the year, the picture of flat house prices seems to have given way to a new downward trend, consistent with the fact that the economy has slipped back into recession."
