The Scio device was backed by about 13,000 people in a successful crowdfunding campaign in 2014.
However, some have complained they are still waiting for their device to be delivered.
Co-founder Dror Sharon told the BBC that 5,000 devices had been shipped.
Mr Sharon has previously described Scio as the first cheap, accessible molecular spectrometer.
It takes an electro-magnetic reading of objects, then compares the result with an online database. It can be used, for example, to distinguish between medicines, or summarise the fat content of a slice of cheese.
During the crowdfunding campaign, backers paid between $150 (Â£115) and $300 for the device, with developer kits costing up to $1,000.
Consumer Physics, the company behind the product, raised $2.7m in the campaign and estimated that devices would be delivered by February 2015.
However, Mr Sharon admitted the firm had experienced delays.
"It has taken more time than we expected," he told the BBC.
"We had to design the technology from the ground up, we had to do some redesigns, and we had some issues with suppliers.
"Each bump in the road took weeks to rectify."
Some backers have expressed concern about the delay on the company's Facebook page, after its crowdfunding page was taken offline.
Visitors are now told the company is facing an "intellectual property dispute", but Mr Sharon said the issue was solely concerning the Scio name.
"It has nothing to do with the intellectual property in the sensor or the optics, it's purely a trademark dispute," he said.
"But Kickstarter has a very careful policy, they took down the page and put up the note - we tried to reason with them, but they have their policy and we respect that."
He said the company was continuing to produce the devices, but had chosen to prioritise deliveries to app developers, to speed up the creation of its app ecosystem.
"We've shipped thousands of these little scanners all over the world," Mr Sharon told the BBC.
"We decided to start shipping to developers first, which has added some delay for Kickstarter backers who were expecting to get the device very early.
"We realise it's late, but we're doing our best to ship as fast as we can. Between a third to a half of our backers have their device."
The maker of a pocket spectrometer, which can scan and identify a variety of objects, says his company is working hard to fulfil outstanding orders.