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Martin O'Neill revealed the full-back was sent for the scan as Celtic assess the extent of the injury.
Johnston had only just returned after missing action since early August because of a hamstring issue. He was introduced against Hibernian on Sunday afternoon, but lasted 20 minutes before going off.
Celtic manager O'Neill said: "He felt something at the top of his hamstring again. It's the same hamstring as before."
Speaking to Celtic TV, O'Neill said staff were unsure how serious the problem might be.
He added: "We're not sure, we're genuinely not sure."
Celtic are hoping the injury is not serious, with the manager saying the club should know more in the next couple of days.
Johnston is unlikely to be fit for Wednesday evening's match against Dundee United. He had replaced Colby Donovan, who took a knock, at Hibernian.
That leaves Anthony Ralston or Jordan Lotomba as choices for the starting line-up. Johnston had been ruled out since going off against Kilmarnock in early August, making Sunday's return his first appearance since then.