Information Minister Moammar al-Eryani said government forces retook Aden's airport, its presidential palace and surrounding areas from forces aligned to the Southern Transitional Council (STC) on Wednesday.
"The National Army & the security forces impose full control over Aden's districts amid great public satisfaction and welcome," he said in a post on Twitter.
He tweeted a video of people holding pictures of President Abd-Rabbu Mansour Hadi as they celebrated in Aden, the temporary seat of his government.
Government forces also secured a military camp belonging to the STC-aligned Security Belt militia in the nearby town of Lahij, said al-Eryani.
There was no immediate comment from the separatists.
The separatists, who seek self-rule, turned on the government earlier in August after accusing a party allied to Hadi of being complicit in a Houthi
on southern forces. After four days of fighting that killed at least 40 people, the separatists took effective control of Aden.
But the fighting in recent weeks between Hadi's forces and separatists has
to open a new front in the complex war in the Arab world's most impoverished country. The two sides are nominal allies in a Saudi-UAE-led coalition fighting the Houthi rebels who control the country's north.
The standoff has also exposed a rift between Gulf allies
and the UAE, which in June scaled down its presence in Yemen under Western pressure to end the devastating war, but continues to support thousands of southern separatist forces.
Residents told Reuters news agency both sides exchanged artillery fire across Aden on Wednesday, but the separatists withdrew from some positions and checkpoints, allowing government forces to reach Aden's central neighbourhoods. Hadi forces were seen securing areas around the presidential palace and the headquarters of Yemen's central bank.
"The State's return to Aden is a victory for all Yemenis," Yemen's Prime Minister Maeen Abdulmalik Saeed said in a statement, urging reform of the security services.
Yemen's interior ministry warned government forces not to take revenge against separatists.
The reported capture of Aden on Wednesday came days after government troops also wrested control of Zinjibar, the capital of the neighbouring province of Abyan, and secured
most of the oil-producing province of Shabwa and its liquefied natural gas terminal in Balhaf.
Nabeel Khoury, the former US deputy chief of mission in Yemen, said it was too early to say if Hadi's government was indeed in control of Aden.
"We're in the midst of very fast-paced events in the south of Yemen with almost zero transparency on the part of the Arab coalition," he told Al Jazeera from Beirut in Lebanon.
"Hadi does not have a real army to be able to retake the south," he said, describing the troops aligned to the government in Aden as "tribal forces from Abyan and Shabwa".
"I'm afraid that what we see is only the beginning of further chaos and perhaps a return to the traditional schism between the western parts of south Yemen and the eastern regions."
Earlier on Wednesday, speaking before the reported capture of Aden, Alkhader Sulaiman, a spokesman for the STC, described Hadi's push on the city as a "cheap, immoral" move "to cause chaos in the city".
"The legitimate government has proven to be incompetent, dysfunctional and is corrupted from the highest-ranking government official to the lowest official," Sulaiman told Al Jazeera from New York.
He said Hadi's government has "no intention of fighting the Houthis".
"They have been in a stalemate ceasefire in Aden with over 250,000 troops for over four years and they have only used these forces to destabilise what has already been liberated by the southern forces in the southern governorates," he said.
South Yemen was a separate state until it merged with the north in 1990. Four years later, an armed secession bid failed to reverse the reunification.
The push on Aden by Hadi's government came days after the Saudi-led coalition called for a ceasefire
and invited both sides to reconciliation talks in Saudi Arabia. The coalition also urged the separatists to withdraw from all government buildings and military bases.
But Hadi's government said it would not participate
in the talks until the separatists cede control of sites they have seized.
Sama'a al-Hamdani, an independent analyst on Yemen, said even if Hadi's forces take control of Aden, there were likely to face challenges.
"The Yemeni government had control of the area for four years and failed to instil some sort of policies that had seemed fair to the population," she told Al Jazeera from Washington DC.
"So even if the Yemeni government captures Aden and the south again, they are going to really have to change their policies and address the concerns of the people, because the secessionist cause was not something that was born over this war - it's a demand they've had way before the war started."
The crisis in the south has also complicated the United Nations
' efforts to implement peace deals elsewhere in the country and pave the way for negotiations to end a war that has killed tens of thousands and pushed Yemen to the brink of famine.
Commenting on Wednesday's developments, a member of the Houthi group called for direct talks between Yemen's warring parties.
"Saudi Arabia won over the UAE which means that the party that wants to destroy Yemen won over the one that wants to divide Yemen," said Mohamad al-Bukhaiti.
"We call on Yemeni-Yemeni dialogue without outside intervention," he told Al Jazeera, rejecting the idea that a solution to the Yemen crisis must come through UN-sponsored negotiations.