Singh, who had resisted eviction and demanded that the government accommodation be converted into a memorial for his father former prime minister Charan Singh, handed over the bungalow to the Central Public Works Department, according to a senior urban development ministry official.
The official said though Singh vacated the bungalow, he is yet to clear the penal rent for his unauthorised stay of 118 days.
The penalty for overstaying is 55 times more than the monthly rent of Rs 3,500 per month.
According to the official, it comes to over Rs 7 lakh now as the penalty will be calculated from June 27.
With the handing over the Type VIII bungalow at Tughlaq Road, the tussle over the sprawling property at Lutyens zone between the government and the RLD
Singh, who lost the elections, was served an eviction notice in June. Civic bodies later disconnected water and power supply to the bungalow.
Singh along with RLD supporters, who staged protests in the city and in Ghaziabad, demanded that the bungalow be converted into a memorial to Charan Singh.
The government, however, rejected the demand, saying the Union Cabinet in 2000 had "banned" conversion of Lutyens' bungalows into memorials.
Ajit Singh accused the BJP government of vendetta but Union Urban Development Minister Venkaiah Naidu said the authorities were bound by rules.
As Congress too supported the demand, Naidu retorted by asking why the RLD leader or Congress had not set up the memorial when they were in government.
Ajit Singh's supporters clashed with police in Ghaziabad on September 18 over the move to evict him from government residence. On September 23, police detained at least 250 protesters to prevent them from gathering at the bungalow for a planned meeting demanding its conversion into a memorial.