The Church Investors Group (CIG), which manages £17 billion of assets, has written to the 350 biggest companies on the London stock market saying it will vote against excessive pay deals.
The Church Commissioners, which handles the Church of England's investment portfolio, has £7 billion worth of assets.
The threat comes ahead of a series of significant company AGM shareholder meetings this year, where nearly half of FTSE 100 businesses are facing binding votes on pay.
Recent figures showed pay for FTSE 100 chief executives soared from £1 million on average in 1998 to £4.3 million in 2015 - much more than the increase in average earnings.
The CIG voted against two-thirds of company pay reports last year, however the votes were advisory rather than binding. Rules have changed since then meaning they can use their shareholder rights to block pay they deem unacceptable.
Adam Matthews, head of engagement for the Church Commissioners and Church of England Pensions Board, said: "Last year saw a number of high-profile votes going against board recommendations and we expect this issue to continue to be high on shareholders' agenda in the 2017 voting season.
"It is vital that companies exercise judgment when recommending executive remuneration packages to shareholders."
