The so-called Crystal Methodist, 66, who was filmed doing a drugs deal in 2013, was last week stripped of the title reverend and the power to lead services for "seriously impairing the mission, witness or integrity of the Church".
While accepting the outcome of disciplinary proceedings, he said he lacked "the same respect for the church" and its handling the incident was not "helpful".
He told Radio 4's Sunday Programme it would be a "lie" to suggest his substance problems were completely behind him.
Mr Flowers was suspended by the church in 2013 following allegations he bought and used illegal drugs.
Coupled with claims of inappropriate expenses payments four years ago, the accusations swelled into a storm of controversy that forced him to step down as chairman of the Co-operative Bank.
"The truth is that I think all of us struggle with issues of addiction and we have different addictions that affect millions of us in this country," he told the programme.
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Former Co-operative Bank boss Paul Flowers claimed he still battles with addiction
The truth is that I think all of us struggle with issues of addiction
Paul Flowers
"I'm not going to tell you a lie that it's behind me totally, because it isn't, but I believe it's now largely behind me, but we still struggle with addiction of different sorts."
He was secretly filmed handing over £300 in cash for drugs in 2013 and admitted being in possession of cocaine, crystal meth and ketamine at Leeds Magistrates' Court in May 2014.
Mr Flowers was fined £400 and ordered to pay £125 in costs.
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The so-called Crystal Methodist was filmed doing a drugs deal in 2013
In his Radio 4 interview, he said his mother's death was a driving force behind his drug use – and admitted his "disaster" of a performance in front of a parliamentary select committee could have been influenced by drugs.
He also addressed his alleged use of male escorts, saying that being at the top of an organisation is "sometimes lonely and very often in need of intimacy".
He added: "I don't apologise for being in that position."
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His ignominious departure from the bank and suspension from the church ultimately made his faith stronger, he claimed.
But he said: "I don't think I have the same respect for the church as an institution. I think that the church generally – and the Methodist church is part of that – is lagging behind on issues affecting LGBT people such as myself."
He added: "In my experience of the last week or so when a press release was issued without my knowledge by the church authorities…(it) was not exactly helpful in relation to the way the church should go about things."
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