Rescue operations, which began on Thursday, have been extended into the weekend with Ghana President John Dramani Mahama declaring three days of national mourning.
Mr Annan took to Twitter on Friday, June 5 to express his sympathies.
“My thoughts are with the victims of the explosion in Accra and their loved ones,” he tweeted.
“May they rest in peace.”
With a signature of ‘KA’, the tweet is one of the few personal ones from the Ghanaian.
Mr Annan is among world leaders who have consoled Ghana on the tragedy.
Togo leader Faure Gnassingbe was in Accra on Friday to join President Mahama tour some of the hard-hit areas