The toll is the highest suffered by government forces in a single incident since they launched a military operation to halt the rebellion in east Ukraine against the country's pro-European leaders and try to prevent the country splitting up.
The defence ministry said the Il-76 plane was shot down in a "cynical" attack by rebels using an anti-aircraft weapon and a heavy-calibre machine gun.
It gave no death toll but Vladislav Seleznyov, spokesman for the military operation in east Ukraine, said: "Forty-nine people were killed. All were Ukrainian military personnel."
The prosecutor-general's office said nine crew and 40 paratroopers had been killed and that the plane was hit by an anti-aircraft missile at 1.10am local time
The Luhansk region is at the heart of the rebellion launched in April by separatists who want Russia to absorb the Russian-speaking east following the annexation of Crimea in March.
Government forces control Luhansk airport but local media said fighting was under way yesterday in the city, control of which is important for patrolling the nearby border with Russia.
The rebels also said the Ukrainian air force had fired on the industrial town of Horlivka, just north of region's main city, Donetsk.
Rebels also shot down a military cargo plane last week, killing three people, and a general was among 14 killed when they hit an Mi-8 transport helicopter on May 29.
Scores of rebels, civilians and soldiers have been killed in the violence since April and more than 100 protesters, most of them seeking closer ties with the West, were killed in clashes with police in February that led to the fall of Ukraine's Moscow-leaning president.
The new clashes last week, in which government forces reclaimed the southeastern port city of Mariupol, threaten tentative peace moves since the new president, Petro Poroshenko, was sworn in a week ago.
The breakdown of talks on a dispute over the price Kiev pays for Russian natural gas has also soured the atmosphere, with Moscow threatening to cut supplies to Kiev tomorrow unless it starts paying its bills.
Russia fears it is losing influence in Ukraine, which was governed from Moscow in Soviet times and is seen by Russians as the cradle of their civilisation, but it denies being behind the uprising. The rebels say they get weapons from army stockpiles and warehouses.
America's State Department claims Russia has sent tanks, heavy weapons and rocket launchers to Ukraine in recent days in support of separatists. The assertion is likely to deepen strains in the worst standoff between Moscow and the West since the Cold War ended.
"We assess that separatists in eastern Ukraine have acquired heavy weapons and military equipment from Russia, including Russian tanks and multiple rocket launchers," State Department spokeswoman Marie Harf said.
Harf earlier told a briefing that a convoy of three T-64 tanks, several MB-21 or "Grad" multiple rocket launchers and other military vehicles had crossed from Russia into Ukraine in the last three days.
"This is unacceptable," she said. "A failure by Russia to de-escalate the situation will lead to additional costs."
Evidence Russia is sending in heavy armour and weapons could encourage the US and the European Union to impose new sanctions on Moscow. So far these are limited largely to visa bans and asset freezes on some individuals, banks and companies.