The pop singer, 27, detailed her "absolutely magical" experience earlier this week, including a visit to the World Holocaust Remembrance Centre in Jerusalem.
Lovato said the trip, which took in other holy sites around the city, had filled "the God-sized hole in my heart".
However, following her social media posts gushing about her visit to Israel, former Disney Channel star Lovato was criticised online for praising the country as it is involved in a dispute over contested land with Palestine.
Lovato has now responded to the backlash, saying she is "extremely frustrated" by the controversy and she never intended to make a political statement.
"I accepted a free trip to Israel in exchange for a few posts. No one told me there would be anything wrong with going or that I could possibly be offending anyone," Lovato wrote on Instagram.
"With that being said, I'm sorry if I've hurt or offended anyone, that was not my intention."
Lovato said she was unaware the trip could result in criticism. "This was meant to be a spiritual experience for me, NOT A POLITICAL STATEMENT," Lovato wrote.
"Now I realise it hurt people and for that I'm sorry."
The singer add she is "sorry I'm not more educated, and sorry for thinking this trip was just a spiritual experience".
She finished the message by writing: "I love my fans, all of them, from all over the world."
Israel is often at the centre of celebrity calls for a boycott.
Earlier this year high-profile British figures including Vivienne Westwood, Peter Gabriel, Roger Waters and Mike Leigh signed a letter calling for the BBC to cancel its coverage of the Eurovision Song Contest, which was held in Tel Aviv.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.
