"Hugo has damaged the medial ligament in his right knee and it doesn't look good," Martinez was quoted as saying on Wigan's official website.
"Having returned from the Copa America tournament in the summer he's [been] looking sharp and enjoying his football and it's the biggest negative to come out of today's game."
The 26-year-old, who helped Colombia reach the Copa America quarter-finals in July, will have a scan on Sunday after being carried off on a stretcher in added time at Goodison Park.
"The scans will give us a final verdict in the week but if it's a rupture of the ligament we're looking at him being out for around nine to 12 weeks so we'll keep our fingers crossed and see if Hugo's body has reacted well to the injury or not."
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