Rev Graham Sawyer from St James Church in Briercliffe was targeted for 13 months before officers issued a woman with a harassment notice in December 2015, putting an end to "countless" attempts to contact him.
Assistant chief constable at Lancashire Police, Terry Woods, said: "While this particular case was some time ago and our practices in dealing with such cases have moved on, we acknowledge the level of service provided to the victim fell short of what could be expected and we apologise for that."
Rev Sawyer first alerted police in November 2014 to his stalker, who would loiter around his church before services started in order to catch him alone.
The 56-year-old told the Lancashire Telegraph the perpetrator incited a "vengeful mob" by spreading false allegations about him, and attendance to his service dropped by up to half by the stalking was happening.
He told the newspaper: "This is about the repeated failings of Lancashire police with my case; it's about the way the police is handling stalking in England and in Lancashire.
"They [police] made things exponentially worse for me, my congregation and for my stalker.
"I would never go to Lancashire police again for help after this."