Phillips has been indefinitely suspended from squad duties following the publication of a series of damaging photos taken in Cardiff city centre.
The 28-year-old Lions scrum-half is seen being restrained by security staff outside a McDonalds at 3am before later being taken away by police, though no arrest was made.
The incident comes soon after Phillips' fellow Wales internationals Gavin Henson and Andy Powell incurred the wrath of their clubs.
While disappointed by such behaviour, Lewis insists they are only isolated incidents that fail to reflect the overall professionalism of the squad.
"There are one or two exceptional things that have happened and one or two individuals who have brought a great besmirch to Welsh rugby," he told Sky Sports News.
"They are very much the exceptions - the majority of players do not behave like this. They are hard-working, dedicated professionals.
"We are now addressing this in a very serious and severe way.
"The action taken - on discovering what took place and what was published in today's press - sends out a message that this sort of behaviour, not only do we not condone it but we condemn it.
"The players will be disappointed by Mike's actions but they will be hardened in their resolve to prove they are a dedicated group of players.
"The impact of this announcement will harden the resolve to do better than we have."
Phillips, who had sealed a move to French Top 14 club Bayonne from the Ospreys earlier in the week, will now be questioned by the WRU who want clarification over the events that took place in the early hours of Tuesday morning.
The photos will cause acute embarrassment to the WRU, who only recently have seen Henson and Powell run into disciplinary problems at their clubs.
Henson was suspended for one week in April by Toulon for fighting with two team-mates and one month later Powell was forced out of Wasps in the wake of a fracas with football fans in a London pub.
Powell was also suspended by Wales in February 2010 after driving a golf buggy up the hard shoulder of the M4 motorway whilst over the legal alcohol limit following the Six Nations win over Scotland.
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