Matthew Yaffe calls the colorful glass pipes he sold in his Allston store “functional art.’’ He describes his shop, where some pieces fetched up to $5,000, as a “glass gallery.’’

Boston police, however, see Yaffe’s artwork differently. They call the glass objects pipes for smoking illegal drugs, and they have charged Yaffe, 32, of Milford, with peddling drug paraphernalia from his shop.

The police raid on his Green Side Up Gallery was one of three since April in Allston, where police have been cracking down on so-called head shops, stores that sell pipes and rolling papers that can be used to smoke marijuana.

The busts were well planned. Officers took photographs of the shops before making their arrests, and interviewed North End tobacconists to bolster their argument that the Allston shops were selling drug paraphernalia.

“We’re not looking to put anyone out of business [who is] running a legitimate business,’’ said Captain James Hussey, who runs the Brighton district. “These places were set up, it appears, just to sell drug paraphernalia.’’

Lawyers for those arrested say the shops were licensed by the city and state to sell the products, and police had no basis for shutting down the shops. But Hussey said two of the shops — neither of which belonged to Yaffe — did not have proper licenses displayed.

Business leaders in Allston, a neighborhood popular with college students and graduates, said they are dismayed by the hard line authorities took.

“Very draconian,’’ said Bob Webber, president of the Allston Board of Trade and owner of Model Hardware. “Troubling to me is that these places were licensed by the city. It was almost like they got the green light, and shortly after opening they got blindsided.’’

After Yaffe’s arrest, Hussey met with Webber and other business leaders at the police station, where Hussey said he would try to come up with guidelines for other glass pipe sellers in the neighborhood who are nervous they could be raided.

The dispute between the business owners and police centers around the state law against drug paraphernalia, which can include bongs and pipes, but also blenders, balloons, and even spoons. The law, however, stipulates that authorities should consider various factors before deciding that such equipment is being used illegally. For example, police should weigh expert opinion on the objects, as well as whether they were found near drugs or had drug residue on them .