George Charamba, a government spokesman, on Saturday said the cause of death was under investigation and local media said Jokonya had been unwell for some time.
Government ministers generally live in Harare but it is not unusual for them to stay in hotels prior to early meetings.
Jokonya, 67, served at the United Nations during the period of controversial land reforms by the government of Robert Mugabe. Those reforms were condemned by the West and blamed for ruining the farming sector.
Mugabe said in a statement: "He stood for this country at the most challenging times of our land reform programme. He took all these challenges in his stride, all the time convinced his country was right, (and) the cause he defended just."