The Department for Environment said one primary location was targeted - the Skripal's Wiltshire home.
Salisbury cemetery, where the remains of the ex-spy's wife and son rest. was not targeted.
The details emerged as the department announced a major clean-up operation was under way across the city "to bring a small number of potentially contaminated sites back into safe use" for residents and tourists.
In total nine sites, three of which are in the city centre, have been identified as requiring some level of specialist cleaning.
Around 190 specialist military personnel from the Army and RAF will support the operation, which is expected to take months.
The 66-year-old former Russian double agent and his 33-year-old daughter were attacked with novichok and were found collapsed on a bench at The Maltings shopping centre on 4 March.
In an analysis of samples taken from the home of the Skripals, the highest concentrations of toxic chemical novichok, thought to be responsible for their poisoning, was found on door handles.
The London Road cemetery, the mall where the pair were discovered unconscious, Zizzi and the Ashley Wood compound where the ex-spy's red BMW 3 series was taken after the attack have been handed back over by the police investigation.
A police cordon at the cemetery was lifted on Tuesday - the first area to be reopened to the public after extensive testing determined it was not contaminated with the deadly poison.
The department's chief scientific adviser Ian Boyd said: "Our approach is based on the best scientific evidence and advice to ensure decontamination is carried out in a thorough and careful way.
"Our number one priority is making these sites safe for the public, so they can be returned to use for the people of Salisbury.
"Thanks to detailed information gathered during the police's investigation, and our scientific understanding of how the agent works and is spread, we have been able to categorise the likely level of contamination at each site and are drawing up tailored plans.
"Meticulous work is required and we expect it will be a number of months before all sites are fully reopened."
A £2.5m fund has already been announced by ministers to support businesses, boost tourism and meet unexpected costs in the wake of the attack.
Last week, the Government's national security adviser said Russian intelligence had been spying on the Skripals for at least five years.
Cyber experts from military intelligence agency the GRU targeted Yulia Skripal's email accounts as far back as 2013, claimed Mark Sedwill, in a letter to NATO secretary general Jens Stoltenberg.
A programme set up in Russia in the 2000s trained personnel from "special units" in the use of chemical warfare agents, he said, including investigating how nerve agents could be administered through door handles.
Russia has continued to deny any involvement in the poisoning and has accused Britain of abducting Ms Skripal, who has been discharged from hospital and taken to a secret secure location by authorities.
Mr Skripal, who is no longer in a critical condition is making good progress and is also expected to be discharged in due course.