The 25-year-old has impressed during his season-long stint at the bet365 Stadium, featuring in 34 of the Potters' 37 Premier League games thus far.
Martins Indi recently admitted that he expects to return to Porto in time for pre-season training, and Hughes is unsure whether he will be able to get any sort of deal over the line for the Netherlands international.
"We are still discussing the deal and speaking to Porto," he told reporters. "Clearly, Bruno is still their player, so we can only dictate and influence that situation up to a point and we have to be patient.
"It's a little bit frustrating I have to say. We are still talking about how we can move it forward, but there's a little bit of an impasse at the moment."
Martins Indi, who featured 30 times for Porto last season, talked earlier this year of his desire to remain in the Potteries.