Saudi Arabia and the United Arab Emirates -- along with Bahrain and Egypt -- cut diplomatic, transport and trade ties with Qatar in June, accusing it of financing terrorism.
Doha denies the charges.
The diplomatic stand-off with 2022 World Cup hosts Qatar has already caused numerous issues for football in the region.
Clubs from Qatar, Saudi Arabia and the United Arab Emirates were drawn to play each other on Wednesday in the group phase of the Asian Champions League, which kicks off in February, but John believes the confederation can weather the political storm.
"The AFC executive committee has made a decision that they would like all of the matches to be played as per the format, and I believe our regulations at AFC are solid enough to deal with any situation as we have done in the past," John told Reuters.
"So we are confident there will be nothing done outside the regulations. The regulations cover every scenario, so we are good.
"We've just finished the 2017 competition and everybody talked about issues and problems and we finished it quite successfully. I think we want to build on the success rather than talk about other issues at the moment."
GROWING IMPACT
The standoff between the nations, which started in June amid accusations by Saudi Arabia that Qatar was sponsoring terrorism around the region, has had a growing impact on sport in Asia.
The Gulf Cup, which is due to be held in the Qatari capital Doha at the end of this month, is under threat with Saudi Arabia and the UAE unlikely to take part.
Qatari broadcaster BeIN Sports, which hold the rights to the confederation's competitions in the Middle East, has also experienced significant disruption to its attempts to attend games in Saudi Arabia and the UAE.
The UAE, meanwhile, asked soccer's world governing body FIFA to change the referee in a World Cup qualifying match during the summer as the appointed official was a Qatari.
Two groups in next year's Asian Champions League could feature clubs from Saudi Arabia, the UAE and Qatar alongside a team from Iran, a nation also in dispute with the Saudis.
The confederation has already had to deal with the fallout from that diplomatic spat, which resulted in games between clubs from the two nations being played at neutral venues during the 2017 Asian Champions League.
"Using the regulations is how we dealt with the case of Saudi Arabia and Iran," said John. "It will be the same way we will deal with any potential scenarios that may come up.
"The exco (executive committee) also decided a very high level delegation will go and explain the situation to all of the affected countries.
"I think it should be ok, so long as we follow the regulations. Any decision can be appealed, so we have a good structure in place."
The AFC said on Thursday that the prize money for the Asian Champions League would be increased in 2018, with the winners set to receive $4 million (£2.9 million), $1 million more than the amount won by Japan's Urawa Red Diamonds this season.
The prize pot for the runners-up has also been improved, from $1 million to $1.5 million.
(Reporting by Michael Church; Editing by Ken Ferris)
