Sometimes the problem that readers point out is not the actual problem. That is, they correctly identify where a problem exists, but they misname or misidentify what is actually wrong. For instance, they will say that a writer uses too many long words, and then when asked to give examples they will point out words that are five or six letters long, which can be puzzling, until you realize that when they say "long words" they really mean "words I am not familiar with." In your case, it may be a problem with pacing and momentum, and not so much that you use long sentences but that you use them in the wrong places in the action of the story, so that you slow things down when you should be speeding them up. (Although I have read some long sentences, by particularly skilled writers, that have a tremendous sense of momentum, for action I agree that shorter sentences tend to work better—though even then, some variety in the length of sentences may keep the writing from coming across as too choppy. )
Also, as some have already pointed out up above, a very long sentence is not necessarily a run-on sentence and a run-on sentence is not necessarily long. A run-on sentence is a particular type of grammatical mistake. It can make the writing clunky, especially if the same sort of error is made again and again and again. Like sentence fragments, which are also ungrammatical, there are places where, for dramatic purposes, a run-on sentence may work, but it has to be done carefully. So you really do need to talk to your beta readers and find out if the problem is really run-on sentences. If it is, you may not have to shorten your sentences; it may be enough to fix the grammatical error. If they mean that your sentences tend to ramble on and and slow things down (or come across as pretentious) then that is what you need to address.