The non-governmental organisation, which calls itself "This is Bahrain", insisted it had no official status though its mission statements say it has the backing of King Hamad.
This is the first public visit by a Bahraini delegation to Israel, which Manama -- like most Arab capitals -- does not recognise.
Reports in Palestinian media said the delegation was banned from visiting the Al-Aqsa Mosque in annexed east Jerusalem yesterday.
The organiser of the trip, however, declined to confirm, and the Islamic body that governs the site said that while no visit took place, they had not explicitly banned them.
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"About one-third of them are Muslims, there are Christians and two Buddhists," he told AFP. "It's not a political visit so there was no request to see politicians."
The visit sparked angry reactions on social media and by other NGOs in Bahrain, especially as it comes within days of US President Donald Trump's controversial decision to recognise Jerusalem as Israel's capital.
This is Bahrain issued a statement - carried by Bahrain's state news agency BNA - insisting the visit was unofficial.
"The delegation represents solely the society and has undertaken the visit on its own initiative."
The NGO, which received its official licence in May, said the trip was part of an initiative to visit several European countries and the United States.
"The initiative... is based on the principle of tolerance and coexistence, an approach embraced by the Kingdom of Bahrain and a feature of its society, and aims to visit Islamic, Christian, Jewish and other holy sites across the world," it said.
A small protest occurred in the Gaza Strip this morning, sparked by apparently false rumours the delegation would visit the Palestinian enclave.
Bahrain's National Islamic Forum branded the visit an act of normalisation of ties with Israel and in breach of "Bahrain's established national principles which reject all forms of normalisation".
A statement from the Boycott, Divestment and Sanctions movement, which calls for a boycott of Israel over its treatment of the Palestinians, "strongly" condemned the cooperation between the "despotic Bahraini regime (and) Israel's regime of occupation and apartheid".
It has, however, recently seen increased behind-the- scenes cooperation with some Arab countries, particularly in their opposition to Iran.