The firm has cracked down on third-party websites such as Pokevision that let players see where characters in the augmented reality game were located.
A tracking feature intended to help players find the colourful creatures has also had its functionality reduced.
The changes have been criticised by many of the game's fans.
Pokemon Go previously showed players a list of nearby creatures, each with a number of footprints beside it representing its proximity to the player's smartphone.
However, the footprints system was criticised because it did not work as intended and it has now been removed.
Unofficial third-party tracking services, such as Pokevision and Pokeradar, have also had their functionality limited.
Pokevision used data from Pokemon Go to create real-time maps that allowed players to locate specific creatures.
Writing on Twitter, its developer said the site had been disabled.
"We wish we had some news for you," Pokevision tweeted.
"At this moment, we are respecting Niantic and Nintendo's wishes."
The removal of the footprints feature, along with the halting of third-party tracking apps, has caused a stir within the game's community.
"It's so ridiculous that a simple feature could be handled this badly and cause all this backlash," wrote member CA_dot on online discussion forum Reddit.
"I always thought Niantic should have fixed the game instead of removing features."
The updated app also adds a warning not to play Pokemon Go while driving, lets players edit their avatar and fixes a number of bugs.
Pokemon Go players have been left disappointed after developer Niantic made significant changes to the app's Pokemon-tracking functionality.