The CBI later presented a charge sheet and a trial is underway at a sessions court in Punjab.
The CBI had arrested G.M. Mir and Raman Mattoo, both ministers in the then Congress-PDP government, besides Iqbal Khandey, the former principal secretary to then chief minister Mufti Mohammed Sayeed.
On Tuesday, the scandal came back to haunt Kashmiri politicians.
Senior PDP leader Muzaffar Hussain Baig submitted a list of what he said were the accused in the case prepared by the CBI. According to Baig, Abdullah's name was 102nd in the list.
'We want an investigation...' Baig told reporters after the tense session but admitted that this was a mere allegation.
'His (Omar Abdullah's) father's name also figures... It is number 38. I did not take his name (in the house) because he (Farooq Abdullah) is not a member of the house,' Baig said.
He claimed that the list handed over to the assembly speaker by him was the same submitted to the state high court by the CBI.
Abdullah senior - NC president and union Renewable Energy Minister Farooq Abdullah - happened to be in Srinagar too to advise his son. He was due to leave for New Delhi but turned back from the airport to advise his son.
A closed door meeting of Omar with his father ended with the Abdullahs going to the governor's residence Raj Bhavan.
'The chief minister is really upset,' said close aide Devender Rana.
'The allegations levelled against him are false and it is now up to the governor to decide whether to accept the resignation or not,' he told reporters.
Tensions in Kashmir spilled over to the national capital too.
CBI officials, while declining to react immediately on whether Abdullah's name figured in the case, said Home Minister P. Chidambaram was likely to make a statement in parliament.
'We are not commenting on this issue just now. The home minister is likely to make a statement in parliament to clarify matters,' said a senior CBI official.
However, highly placed CBI sources hinted that Abdullah's name did not come up during the course of investigation.
As Abdullah became the talking point of the nation and people argued about the merits of his move, ally Congress also came out in his favour.
'Omar stands on high moral ground,' said state Congress chief Saifuddin Soz. 'He will fight to prove his innocence.'