Consumption, investment and imports were all weaker.
Meanwhile, the government's contribution to GDP failed to show much improvement on the first quarter. The government said it spent less than 40 percent of its budget up through June, with capital expenditure particularly weak.
"We expect growth in the second half to pick up on the back of investment, although we don't think government infrastructure spending will be as big as we initially expected," said Leo Putra Rinaldy, an economist at Mandiri Sekuritas in Jakarta.
"The government is facing challenges in revenue collection, which mean there could be spending cuts to control the deficit. Those spending cuts could come from infrastructure spending," he added.
Read MoreAsian shares off morning lows, but Shanghai, Sydney lag
Widodo's nine-month-old administration has failed to deliver significant economic reforms, and the central bank is poorly placed to boost the economy, with inflation rising and the rupiah vulnerable to outflows once U.S. rates rise.
On Tuesday Bank Indonesia Governor Agus Martowardojo said authorities were closely watching the risk of a further slowdown, while noting the uncertainties posed by an anticipated rise in U.S. interest rates that will probably suck money away from emerging markets like Indonesia.
Although the government had not succeeded in improving spending in the second quarter, Finance Minister Bambang Brodjonegoro still believes GDP growth will rebound significantly on the back of higher fiscal spending.
"(Capital spending) may reach 80-85 percent which would make growth in the second half better," he said on Tuesday.
Read MoreEruption of Indonesian volcano sparks travel chaos
Brodjonegoro also said some fiscal policies were more effective in the second half, including tax incentives to attract investment, and a hike in the threshold of income tax to drive up people's purchasing power.
But analysts remained sceptical.
"Looking ahead, while we don't think growth will slow further, we don't see scope for much of a rebound either. Lower commodity prices, which have led to a slump in export revenue and a sharp deterioration in Indonesia's terms of trade, will continue to weigh on the economy," said Gareth Leather, an analyst with Capital Economics in London.
The government expects GDP growth of 5.2 percent this year, whereas the median forecast from a Reuters poll of analysts was for growth of 4.9 percent.