The discovery was made during an unannounced visit to HMP Bronzefield near Ashford, Surrey, in April.
Nick Hardwick, the chief inspector of prisons, said it amounted to "cruel, inhumane and degrading treatment".
The prison's director said it would only segregate a prisoner if it felt there was no other option available.
Charlotte Pattison-Rideout, director of HMP Bronzefield, Sodexo Justice Services, said the prison had taken on board the recommendations made in the report and had already started to address them. She added that the prison's policy was always to seek reintegration where possible.
Mr Hardwick said some of the issues identified in the report needed "a fundamentally different approach" at national level.
In the inspection report, he said: "We were dismayed that the woman who had already been in the segregation unit for three years in 2010 was still there in 2013.
"Her cell was unkempt and squalid and she seldom left it.
"Although more activities had been organised for her and better multi-disciplinary support was available, she still had too little to occupy her.
"Her prolonged location on the segregation unit amounted to cruel, inhumane and degrading treatment - and we use these words advisedly."
Mr Hardwick said the treatment and conditions of other women held for long periods in segregation was "little better".
He said: "Much of this was outside the prison's direct control and required a national strategy for meeting the needs of these very complex women - as exists in the male estate."
But he added that Bronzefield itself needed to do more to "ameliorate the worst effects of this national failure".
The report calls for a policy to help manage women "with complex needs who cannot be supported in the prison's normal location".
Frances Crook, chief executive of the Howard League for Penal Reform, said: "This shocking case of treatment, which appears to amount to torture, in an English prison should shame ministers who tolerate the over-use of custody for women and consequent poor treatment.
"Her Majesty's chief inspector is absolutely right that specialist care outside of the prison walls needs to be developed for the handful of women who pose particular challenges."
The report said arrangements for transporting prisoners to and from the prison were unacceptable.
The report said women were carried in vehicles with men and spent long periods in the van, possibly because they had to wait while male prisoners were dropped off first.
Some complained they felt unsafe on the trip, it added.
Positives identified by the inspectors included practical resettlement services; good reception, first night and induction arrangements; and very good support for women with substance misuse problems throughout their prison stays.
Juliet Lyon, director of the Prison Reform Trust, said: "The Chief Inspector reports that staff are doing their best to respond to the needs of women at Bronzefield, many of whom are in poor mental and physical health, addicted to drugs and drink and traumatised by separation from their children.
"But why in this day and age are women with such complex needs transported like cattle and dumped in prison, where one of the most damaged women is left to rot in some form of solitary confinement for six years?
"We are quick to condemn cruel, inhumane and degrading treatment of people in prison in other countries, now government must act to put right failings in our own women's justice system."
Ms Pattison-Rideout, said: "We have taken on board the recommendations made in the report and have already started to address these. We will continue to work towards further improving the quality of our services at Bronzefield.
"We cannot comment on individuals. However, we would only segregate a restricted status prisoner with complex needs for any length of time if we felt that there was no other option available, but our policy is to continually seek reintegration wherever possible.
"The report acknowledged the lack of a national strategy to manage women with such complex needs.
"We have been working closely with the National Offender Management Service on how to better support restricted status prisoners, and we await the outcome of the forthcoming review of the women's custodial estate."
An inmate at a women's prison was held in segregation for more than five years, an inspection report has revealed.