Adani Group flagship Adani Enterprises closed down 6.3% after plunging as much as 25%, its steepest fall in nearly a decade.
The freezing of the three accounts was first flagged in an article in India's Economic Times on Monday.
The Adani Group firms involved rejected reports about the National Securities Depository Ltd (NSDL) freezing the funds' accounts as "blatantly erroneous" in identical statements issued to stock exchanges.
The NSDL website showed it had frozen as of May 31 the accounts of Albula Investment Fund, Cresta Fund and APMS Investment Fund without citing a reason.
The Adani firms said they had received an e-mail from the "Registrar and Transfer Agent" dated June 14 saying "that the Demat Account in which the aforesaid funds hold the shares of the company were not frozen".
The NSDL and India's securities regulator SEBI did not respond to requests for immediate comment.
But a senior NSDL official said the depository had frozen accounts of the funds that hold certain other securities and not those holding Adani company shares, adding that freeze was "not new".
"Foreign portfolio investors generally have one account. But in certain circumstances they can have multiple accounts. In this case, the funds hold at least more than one account," said the official, speaking on condition of anonymity because he wasn't authorised to speak publicly on the issue.
Reuters was unable to reach the funds for comment.
Shares of Adani Ports ended down 8.5% after falling as much as 19%.
While Adani Green Energy clawed back most losses to end slightly lower, Adani Total Gas, Adani Transmission and Adani Power shed 5%.
Graphic: Adani group's shares share tank on Monday -
The funds are among the top foreign investors in Adani group companies, based on data from stock exchanges and company reports.
An email sent by an Adani executive to NSDL, reviewed by Reuters, showed Albula and Cresta had cut their stakes in Adani Total Gas, Adani Transmission and Adani Enterprises as of June 11, compared with holdings on March 31, based on National Stock Exchange data.
Albula had cut its cumulative stake by nearly a fourth, while Cresta had cut by nearly a third its total stake in the three companies.
APMS had slightly increased its stake in Adani Total Gas and Adani Transmission and maintained stake in Adani Enterprises, the email showed.
Adani Enterprises stock has risen more than 10-fold in the past year to Friday, in a broad surge in shares in Adani Group companies that has made Adani the second richest Asian, behind Mukesh Ambani of oil-to-telecom conglomerate Reliance Industries.
($1 = 73.1680 Indian rupees)
(Reporting by Sudarshan Varadhan; Additional reporting by Nallur Sethuraman in Bengaluru, Abhirup Roy in Mumbai; Graphics by Nidhi Verma; editing by Emelia Sithole-Matarise, Jason Neely and Jane Merriman)
By Sudarshan Varadhan and Abhirup Roy