Clementine D'souza, 45, principal of Vivekananda Sankul of Sanpada, who had gone missing last week, was found murdered in Pune rural area on November 2.
The police have arrested Sagar Kathor, 21, a driver and a resident of Sanpada, charging him with the murder.
D'souza is survived by her 18-year-old daughter.
The principal was a resident of Panchratan society in sector 5 of CBD Belapur. A missing person's case was filed by her family with the Turbhe police on November 1.
Navi Mumbai deputy commissioner of police (zone 1) Ashok Dudhe said: “We were investigating the matter when we were contacted by the Vadgaon Maval police of Pune rural jurisdiction saying they had found a woman's body which matched the description of the missing person. The body was found in a gutter near National Highway 4.”
A murder case was registered against unknown persons on November 3.
When investigations were on, the accused Kothar, a resident of Gurudutt society in Sector 4 of Sanpada, where the school is also located, came under the scanner.
His neighbours and those in his locality told the police that he was close to D’souza. Sensing he was in trouble, Kathor went to Turbhe police station on Sunday and confessed his crime. He was immediately arrested.
Superintendent of police Pratap Dighavkar of Pune rural police said: “When we found the body, it had hand marks on the victim's neck clearly indicating that she was strangulated."
He added: “Kathor has confessed to his crime. During interrogation, Kathor said that he had killed her in Kharghar and that he had transported her body to Pune via NH-4 to dispose of the body."
Dighavkar added, “Kathor has claimed that he had an affair with D'souza and he had killed her due to some disagreement. However, we cannot confirm the affair angle.”
Kathor was produced in a court and has been remanded to police custody until November 18. Dighavkar said: “Investigations are on and we will try to find out the exact reason behind the murder.”