The country has now seen two consecutive quarters of declining growth, the usual definition of recession.
Its vital oil industry has been hit by weaker global prices, according to the Nigerian Bureau of Statistics (NBS).
But the government says there has been strong growth in other sectors.
Crude oil sales account for 70% of government income.
The price of oil has fallen from highs of about $112 a barrel in 2014 to below $50 at the moment.
Outside the oil industry, the figures show the fall in the Nigerian currency, the naira, has hurt the economy. It was allowed to float freely in June to help kick-start the economy, but critics argued it should have been done earlier.
The government, however, has found some positive news in the figures.
"There was growth in the agricultural and solid minerals sectors... the areas in which the federal government has placed particular priority," said presidential economic adviser Adeyemi Dipeolu.
Nigeria, which vies with South Africa for the mantle of Africa's biggest economy, is also battling an inflation rate at an 11-year high of 17.1% in July.
"A lot of Nigeria's current predicament could have been avoided," said Kevin Daly from Aberdeen Asset Management.
"The country is so reliant on oil precisely because its leaders haven't diversified the economy.
"More recently, they have tried, and failed, to prop up the naira, which has had a ruinous effect on the country's foreign exchange reserves and any reputation it might have had of being fiscally responsible."
This economic recession comes as no surprise to millions of Nigerians. Many say they've never known it so tough.
The slump in global oil prices has hit Nigeria hard. The government depends on oil sales for about 70% of its revenues.
But critics say government policies made a bad situation even worse. The decision to delay devaluing Nigeria's currency meant many businesses struggled to get foreign currency to pay for imports, which had a cooling effect on the entire economy.
Following enormous pressure, the government changed tack this summer, allowing the naira to float.
That's led to a spike in inflation, but the hope is that it will attract foreign investors. The government also says the country needs to import less: it wants to see more products made in Nigeria.

Her husband, Arif Yunus, was given seven years on similar charges. They have been in prison since their arrest nearly a year ago.
Both still face separate charges of treason, which carries a life sentence.
The couple say the case was politically motivated. Azerbaijan has repeatedly jailed human rights activists.
President Ilham Aliyev has ruled Azerbaijan since 2003 and has cracked down hard on political opponents.
Both Leyla, 59, and Arif Yunus are in poor health - she has diabetes and hepatitis C, while he has a heart condition and has suffered two strokes.
US-based Human Rights Watch condemned their prosecution as a "despicable political show trial".
Levan Asatiani, an Azerbaijan researcher at Amnesty International, said "the judicial system has once again revealed itself to be no more than a cynical tool by which President Ilham Aliyev crushes any dissent".
In a statement to the BBC the Azerbaijan government said the court process in the case was "open and free". It also said "the independence of judiciary and the rule of law have been fully guaranteed" in Azerbaijan.
Leyla Yunus was found guilty of fraud, illegal entrepreneurship, tax evasion and falsifying official documents.
She is director of the Institute for Peace and Democracy, a human rights group founded in 1995. It has worked with the Council of Europe - Europe's leading human rights watchdog - and other international bodies, informing them about actions to stifle political dissent in Azerbaijan.
Mrs Yunus had been pressing for reconciliation between oil-rich Azerbaijan and neighbouring Armenia, to defuse their frozen conflict over Nagorno-Karabakh.
Armenian forces took control of the disputed territory in 1994 soon after the break-up of the Soviet Union. But sporadic clashes continue between them and nearby Azeri forces.
(Update 20 August: This article was amended to add the official viewpoint of the Azerbaijan government.)
Nigeria has slipped into recession, with the latest growth figures showing the economy contracted 2.06% between April and June.
[NEXT_CONCEPT]
A prominent human rights activist in Azerbaijan, Leyla Yunus, has been sentenced to eight-and-a-half years in prison for fraud and tax evasion.