Sure it can. If a creature with innate spell-like abilities blows his fort and will saves when hit with a baleful polymorph he loses his innate spell-like abilities.Temporarily, yes. That's like saying you can lose innate spell-like abilities by stepping into an anti-magic zone.
Let me rephrase, then, for the pedants:
There is no way to permanently and irrevocably lose innate spell-like abilities short of intervention by a deity.
Technically that's true of a cleric too. No matter what the cleric does he wont loose the domain power unless the god he worships/(ed) stops granting it. Thus intervention of a diety.
I'd say spell immunity works fine to stop spell like powers even ones without clear corrisponding spell.
Zurai, note: I edited my previous post (I'm a slow typist)
It seems odd that whether or not spell immunity works on a spell-like ability is determined by whether or not the ability in question is "innate" or not.It's not -- or not ONLY determined by that, at least. The ability also has to have a level or level equivalent.
Let me elaborate… it strikes me as odd that the designers would intentionally add this particular layer of complexity in this case. If they wanted to include spell-like abilities, it seems counter-intuitive to differentiate them further than what the description states (that you can only target spell-like abilities that duplicate an actual spell [i.e. spell immunity would work against a spell-like ability that grants the fire ball spell, but not against the Dazing Touch domain power]). The word "innate" is what's throwing things off, and as I said in my previous post, taking into consideration all the new spell-like abilities available, this situation, seems ripe for an eventual errata.
To me, it seems that this issue probably would not have arisen but for the inclusion of all the new spell-like ability powers of clerics and wizards in the new rules. Few, if any spell-like abilities existed for classes, when the original text for spell immunity was written.Actually, there were quite a few. Bards, Paladins, Arcane Archers, Archmages, Blackguards, Heirophants, and Shadowdancers all are classes from the core rules and all have spell-like abilities.
True, I hadn't taken PRCs into consideration. I recant my last sentence in the statement above. However, several of these spell-like abilities are not valid targets of spell immunity anyway… Paladin's special mount for instance. And of the ones that are valid, they nearly all duplicate a spell.