Jaising accused the government of targeting the couple for the human rights work they have done.
The action came almost a month after the CBI registered a case against Mumbai-based NGO Lawyers Collective and its President Anand Grover for alleged violation of the Foreign Contribution (Regulations) Act (FCRA), criminal conspiracy and criminal breach of trust.
The CBI searches, which started around 5 a.m. in both cities, followed a Home Ministry report.
Indira Jaising is not named in the CBI FIR. According to the CBI, unknown officer-bearers and functionaries of the NGO, private persons and public servants have also been made accused in the FIR.
The CBI officials said the searches took place at the residence and office of Jaising in Nizamuddin East in Delhi.
The CBI team also searched the offices of Lawyers Collective in Mumbai and residence of Grover.
A senior CBI source said during searches, they have recovered several incriminating documents supporting the travel expenses of Jaising being borne by the Lawyers Collective.
Speaking to reporters in Delhi, Jaising said, "Grover and I are being targeted for the human rights work that we have done over the years."
The Home Ministry report said the NGO was registered for carrying out social activities and it received Rs 32.39 crore from 2006-07 to 2014-15.
The violation of the FCRA was noticed in 2010, the complaint said.
The CBI case says Jaising got a remuneration of Rs 96.60 lakh from Lawyers Collective to travel abroad.
Delhi Chief Minister Arvind Kejriwal and the Trinamool Congress condemned the CBI raids.
"Let the law take its own course, but subjecting veterans who have all through their lives fought for upholding the rule of law and constitutional values is a clear vendetta," Kejriwal tweeted.
"The CBI raid at the residence of Indira Jaisingh and Anand Grover is yet another example of the many instances of vendetta. This government is harassing citizens and all voices of opposition. This is a Super Emergency," Trinamool Congress Rajya Sabha MP Derek O' Brian said in a tweet.
( With inputs from IANS )