Some users said they were leaving the music service over changes in its terms and conditions.
The new terms included access to pictures, contact phone numbers and sensor data stored on the user's smartphone.
He promised an "update" to the new policy in order to clarify it but did not suggest that the terms themselves would be changed.
"We should have done a better job in communicating what these policies mean and how any information you choose to share will - and will not - be used," Mr Ek wrote.
He said Spotify would not access or import people's photos, contacts, sensor or GPS data without their permission.
Minecraft creator Markus Persson, aka Notch, had tweeted to his 2.4 million followers earlier that he was cancelling his account.
Sensor data, such as how fast the user's phone is moving, helped the Swedish firm develop Spotify Running, a new feature that tailors music playlists to physical activity.
"Spotify is constantly innovating and evolving its service to deliver the best possible experience for our users. This means delivering the perfect recommendations for every moment, and helping you to enjoy, discover and share more music than ever before," Spotify said in an earlier statement.
"Throughout, the privacy and security of our customers' data is - and will remain - Spotify's highest priority.
"We will always ask for individual permission or clearly inform you of the ability to opt out from sharing location, photos, voice and contacts."
The firm has 75 million active users and 20 million subscribers in 58 countries, according to its own figures.
The terms and conditions also state that it is up to the user to ensure that people listed in the contacts list on their handset are happy for their phone number to be shared with the music platform.
There had been some angry reaction to the changes.
"Like a jealous ex, Spotify wants to see (and collect) your photos and see who you're talking to," wrote Wired magazine.
"I'm now considering whether the £10 I pay for a premium membership is worth it, given the amount of privacy I'd be giving away by consenting," wrote Forbes reporter Thomas Fox-Brewster.
Markus Persson tweeted the company directly.
"As a consumer, I've always loved your service. You're the reason I stopped pirating music. Please consider not being evil," he wrote.
"We want to be as open and transparent as possible when it comes to how we describe our business, how we work with advertisers, what information we collect, and what we do with it," the post said.
"We also want to make sure our terms are up-to-date with all the latest features we are offering."