Yogendra Yadav alleged that the raids were a form of intimidation by the government.
Tax raids at the hospitals and homes of Yogendra Yadav's sisters in Haryana ended after 27 hours on Thursday with the Income Tax department linking the searches to a larger investigation against fugitive jeweler Nirav Modi.
Officials of the Income Tax department claim they were sifting through crores in sales by Nirav Modi and found that Yogendra Yadav's nephew had bought jewellery worth about Rs 6 lakh - more than half of it paid in cash.
Tax officials claim to have seized during the raids Rs 29 lakh and evidence of tax evasion in the form of cash receipts of hospital transactions.
The family said in a statement to NDTV: "We cannot judge why the raids happened. Our only connection with Nirav Modi is that a ring worth Rs 3.5 lakh was bought from a Nirav Modi jewellery showroom in Delhi in February 2017. All the money and assets involved came from our taxable income".
Nirav Modi is wanted in India for a massive loan fraud worth Rs 13,000 crore.
Yogendra Yadav, who set up the Swaraj Abhiyan outfit after his bitter exit from the Aam Aadmi Party (AAP) in 2015, alleged in tweets that the raids were a form of intimidation by the government because of his campaign in support of farmers.
"This raid has been conducted just two days ahead of the meeting for campaign for higher Minimum Support Price by Farmers organisations on 13 and 14 July. The more they try to threaten us, the more our voice will become stronger for farmers' rights," said the psephologist-turned-politician.
Many opposition parties have backed Mr Yadav and targeted the BJP-led central government. Among them is his estranged former AAP colleague Arvind Kejriwal.
Mr Yadav said more than 100 officials from Delhi raided the hospital and "detained" all the doctors, including his sisters, brother-in-law and nephew, in their chambers.
"Hospital sealed, including ICU for new-born babies. A clear attempt to intimidate. Modiji you can't silence me," tweeted the Swaraj Abhiyan leader.
The statement, issued by the family, later clarified: "The hospitals were never shut down. All main surgeries and emergency functions took place. Some minor functions did get affected because new billing had been stopped for some time. Yogendra could not contact us since we were not allowed to fully use our phones during the raids. Hence, some misinformation may have taken place regarding the functioning of the hospitals being stopped completely."
According to one estimate, sales by Nirav Modi amounted to nearly Rs 6,000 crores in 2016. The tax department is yet to give clear details on why a Rs 3.5 lakh cash transaction by the Yadav family was specifically chosen as a basis of sweeping raids.