The contraction, which follows on the heels of a decline in growth in the first quarter, will be a sharp blow for Prime Minister Matteo Renzi's government as the country struggles to pull out of the worst recession since World War II.
The official Istat data agency said in an initial estimate that the gross domestic product had shrunk by 0.3 percent from output in the same period last year, hitting the lowest second-quarter level for 14 years.
The result was worse than expected, with analysts having forecast between a 0.1 percent contraction to a 0.1 percent increase in growth.
Italy "is struggling to pull out of the recession because it is a very deep one," Finance Minister Pier Carlo Padoan said in an interview with Il Sole 24 Ore daily.
He insisted, however, that the country would not breach the European Union's three percent deficit ceiling "either in 2014 or 2015."
"There are no shortcuts to a return to growth. We have to remove the obstacles in our path through reforms," he said.
Renzi, who came to power in February after ousting his predecessor for failing to do enough to revive growth in Italy, has made difficult and often contentious reforms the keystone of his leadership.
The deep, two-year recession had formally ended in the fourth quarter of last year with growth of 0.1 percent.