Al-Khelaifi was speaking before their Champions League round 16 first-leg win on Tuesday night.
Any bridges that did exists between the clubs have been almost entirely burnt by the Kylian Mbappe affair, with the Spanish club aggressively pursuing the France international and PSG playing hardball.
"I'm not going to hide it, we barely have any relationship with Real Madrid," Al-Khelaifi told Canal Plus in France.
"I'm not going to remind you what happened... I believe in football being accessible for smaller clubs; they don't think the same."
Al-Khelaifi also spoke of his pride at what has been achieved in Paris since the Qatari takeover but he is aware there is much unfinished business yet.
"Yes, we're proud of what we've done [raising PSG to Madrid's level]" said Al-Khelaifi.
"We still haven't met our objectives. It will take time, we know that."