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General secretary Gianni Infantino said in London on Thursday that the holders, alongside the league champions from UEFA's seven top-ranked nations, will be placed in pot one for the 2014-15 competition.
Teams are currently seeded based on their UEFA coefficient, which depends on performances in the Champions League and Europa League rather than domestic competitions.
It has led to anomalies, such as the fact that Premier League holders City were placed in Pot Two this season, while Arsenal, who consistently finish third or fourth, remain in Pot One.
The current system has led to the club's current tough draw which seems them pitted in a group with Bayern Munich, Roma and CSKA Moscow, having already faced the German giants twice at the same stage over the past four seasons, as well as Real Madrid in the 2012-13 campaign.
The change of policy has already been agreed on the basis of 'sporting merit', however, and just needs to be rubber-stamped by the executive committee.
'It will ratified later on by the executive committee but it’s a clear recommendation of the club competition’s committee that the seeding system changes in this respect as from next season,' Infantino told Sky Sports.
'It was maybe a bit difficult to understand especially in the last few years where the winner of the national league was not necessarily the best-ranked club.
'It happened in France and it happened in England, people had difficulties in understanding how the champion of a country is in a lower pot than the third ranked in that country.
'Football is about winning, it’s about competition it’s about sporting merit. I think it’s kind of a natural thing to give to those who have won a competition a special treatment like this.'
City have earned just one point from their opening two Champions League matches so far this season, losing 1-0 at Bayern before a 1-1 draw at home to Roma, but captain Vincent Kompany is not yet panicking over a potential early exit.
With their next two matches coming against Group E bottom-dwellers CSKA, who have lost both their games, the Belgium international remains confident that the club can make a quick turnaround and go into their final fixtures against their main rivals in a comfortable position.
'It could go any way really,' he told M.E.N. Sport. 'Roma have to play Bayern now and one of the teams will lose points, if my maths is correct. And that will probably leave us with an opportunity to get closer again.
'We really hope we can get the six points against Moscow then go into those last two games.
'We have to win both Moscow games – it’s safe to say that. But doing so will not just open up the door for second place, but first place as well. It’s going to be close.
'I don’t think you can really aim for second place – but if you get into contention to go into the next round, I think you will be very close to first. It’s that kind of group.'