The Afghan president hailed the army through a video conference to the military commanders in Kunduz Province on Thursday.
He promised to boost coordination among all security institutions in order to prevent the Taliban from taking over any other city in the future.
Ghani said terrorists from Tajikistan, Uzbekistan and Pakistan had also been involved in the recent offensive on the city.
Ghani has also promised to form a fact-finding mission to investigate the fall of Kunduz to militants, warning that any official who has shown negligence in duties or did not take their job seriously would be punished severely, Press TV reported.
Hundreds of Afghan troops entered the center of Kunduz on Thursday after an overnight counter-offensive.
Some local residents and witnessed said Afghan troops have recaptured the city center only and that fighting continues in other areas still controlled by the Taliban.
Fierce gun battles and explosions were still echoing in parts of the city on Thursday evening. The streets are still littered with bodies and charred and mangled vehicles.
Meanwhile, Zabihullah Mujahid, the Taliban spokesman, has said that militants were holding their ground in the volatile city. However, some militant sources have admitted that Taliban were conducting a strategic retreat from Kunduz.
On September 28, the militants overran the city after entering the province from three directions. Officials confirmed that the Taliban had stormed government buildings and taken over a state-run hospital.
Afghan officials say the militants also freed hundreds of prisoners, including Taliban commanders.
Kunduz Province is strategic as it is located on a crossroad that connects key regions of the country. It is also along the country’s border with Tajikistan and could offer the militants the opportunity to establish a base in the country’s north.