Mr Khaira was last week seen to back the campaign for a referendum on Khalistan in 2020, giving other parties in Punjab a handle to attack AAP chief Arvind Kejriwal.
Pummelled for the comment, the AAP leader had then said that though he was not a votary of 2020 referendum seeking a separate homeland for Sikhs "but I don't hesitate to say that it is a result of a consistent policy of bias, discrimination and persecution of Sikhs ever since partition, be it attack on Darbar Sahib, genocide of Sikhs in 1984 etc!"
The reprimand appeared to have an impact. After his meeting, Mr Khaira said he had explained to Mr Sisodia that he was against the 2020 referendum. "I had never supported the referendum," he said.
The Akali Dal, which ruled Punjab for a decade before it lost the state last year, had led the offensive against Arvind Kejriwal along with the Congress and the BJP. Union Minister Harsimrat Kaur Badal had claimed that Mr Kejriwal appeared to have extended his "tacit support" to the separatist plan because he hadn't contradicted his party leader's statement.
The AAP leadership in Delhi, which had been in the middle of a bitter battle with the Delhi Lieutenant Governor, hadn't spoken about the raging controversy because they didn't want to be distracted.
Mr Khaira was also told to send across a formal explanation for his statement through the party's Punjab unit, which has already distanced itself from the controversial statement.
The BJP leader in Punjab Anil Sarin had demanded that Mr Khaira, who became the leader of opposition in the Punjab assembly, be sacked from the post and Chief Minister Amarinder Singh register a case against him.
Chief Minister Captain Singh didn't go that far but he did condemn Mr Khaira for backing secessionism with his categorical support for Sikh Referendum 2020, conceived by radicals for the creation of Khalistan.
Mr Khaira was among AAP's prominent leaders in Punjab who had lashed out at Arvind Kejriwal for taking the apology route to end defamation cases filed by Akali leaders. Mr Khaira had then called Arvind Kejriwal's apology to an Akali Dal leader a "meek surrender".
Follow NDTV for latest election news and live coverage of assembly elections 2019 in Maharashtra and Haryana.
Subscribe to our YouTube channel, like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.