The woman had approached the court after multiple foetal abnormalities were detected when she underwent sonography after 22 weeks and four days of gestation.
The diagnosis of neurological diseases in her foetus prompted the woman to seek termination of pregnancy. She had to approach the court, as under the law, abortions are prohibited after 20 weeks of pregnancy.
A division bench of justices S M Kemkar and G S Kulkarni had last week ordered a panel of doctors from state-run J J Hospital to examine the woman and submit a report.
The bench, after perusing the report, today said the doctors have come to the conclusion that there are serious deformities in the foetus and continuing with pregnancy would cause harm to the mother.
"We have gone through the exhaustive report and opinions of medical experts. After evaluation of the petitioner, the report has concluded that there are multiple serious neurological and skeletal abnormalities in the foetus," Mr Kemkar said.
It seems certain from the report that if the pregnancy is continued, the baby would have a limited life and may not even grow into an adult, he said.
"Hence, we deem it appropriate to permit the petitioner to undergo medical termination of the foetus. We direct the procedure to be performed tomorrow at the J J Hospital," the court ordered.
The court today also sought to know if the government has formed medical committees and prepared medico legal guidelines for a permanent mechanism for the termination of pregnancy beyond 20 weeks in exceptional cases involving rape survivors and women with abnormal foetus.
The advocate, appearing for the Union government, informed the high court that the government has instructed all state governments to set up district-level committees, as mandated by the Medical Termination of Pregnancy Act.