Wikipedia Scanner allegedly shows that workers on the agency's computers made edits to the page of Iran's president.
It also purportedly shows that the Vatican has edited entries about Sinn Fein leader Gerry Adams.
The tool, developed by US researchers, trawls a list of 5.3m edits and matches them to the net address of the editor.
Wikipedia is a free online encyclopaedia that can be created and edited by anyone.
Most of the edits detected by the scanner correct spelling mistakes or factual inaccuracies in profiles. However, others have been used to remove potentially damaging material or to deface sites.
Mistaken identity
On the profile of Iranian President Mahmoud Ahmadinejad, the tool indicates that a worker on the CIA network reportedly added the exclamation "Wahhhhhh!" before a section on the leader's plans for his presidency.
A warning on the profile of the anonymous editor reads: "You have recently vandalised a Wikipedia article, and you are now being asked to stop this type of behaviour."
Other changes that have been made are more innocuous, and include tweaks to the profile of former CIA chief Porter Goss and celebrities such as Oprah Winfrey.
When asked whether it could confirm whether the changes had been made by a person using a CIA computer, an agency spokesperson responded: "I cannot confirm that the traffic you cite came from agency computers.
"I'd like in any case to underscore a far larger and more significant point that no one should doubt or forget: The CIA has a vital mission in protecting the United States, and the focus of this agency is there, on that decisive work."
Radio change
The site also indicates that a computer owned by the US Democratic Party was used to make changes to the site of right-wing talk show host Rush Limbaugh.
The changes brand Mr Limbaugh as "idiotic," a "racist", and a "bigot". An entry about his audience now reads: "Most of them are legally retarded."
We really value transparency and the scanner really takes this to another level 
The IP address is registered in the name of the Democratic National Headquarters.
A spokesperson for the Democratic Party said that the changes had not been made on its computers. Instead, they said that the "IP address is the same as the DCCC".
The DCCC, or Democratic Congressional Campaign Committee, is the "official campaign arm of the Democrats" in the House of Representatives and shares a building with the party.
"We don't condone these sorts of activities and we take every precaution to ensure that our network is used in a responsible manner," Doug Thornell of the DCCC told the BBC News website.
Mr Thornell pointed out that the edit had been made "close to two years ago" and it was "impossible to know" who had done it.
Voting issue
The site also indicates that Vatican computers were used to remove content from a page about the leader of the Irish republican party Sinn Fein, Gerry Adams.
The edit removed links to newspaper stories written in 2006 that alleged that Mr Adams' fingerprints and handprints were found on a car used during a double murder in 1971.
The section, titled "Fresh murder question raised" is no longer available through the online encyclopaedia.
Wikipedia Scanner also points the finger at commercial organisations that have modified entries about the pages.
One in particular is Diebold, the company that supplied electronic voting machines for the controversial US election in 2000.
In October 2005, a person using a Diebold computer removed paragraphs about Walden O'Dell, chief executive of the company, which revealed that he had been "a top fund-raiser" for George Bush.
A month later, other paragraphs and links to stories about the alleged rigging of the 2000 election were also removed.
The paragraphs and links have since been reinstated.
Diebold officials have not responded to requests by the BBC for information about the changes.
Web history
The Wikipedia Scanner results are not the first time that people have been uncovered editing their own Wikipedia entries.
Wikipedia Scanner may prevent an organisation or individuals from editing articles that they're really not supposed to
Earlier this year, Microsoft was revealed to have offered money to experts to trawl through entries about the company and its products to make corrections.
Staff at the US Congress have also previously been exposed for editing and removing sensitive information about politicians.
An inquiry was launched after staff for Democratic representative Marty Meehan admitted polishing his biography
The new tool was built by Virgil Griffith of the California Institute of Technology.
It exploits the open nature of Wikipedia, which already collects the net address or username of editors and tracks all changes to a page. The information can be accessed in the "history" tab at the top of a Wikipedia page.
By merging this information with a database of IP address owners, Wikipedia Scanner is able to put a name to the organisation and firms from which edits are made.
The scanner cannot identify the individuals editing articles, admits Mr Griffith.
"Technically, we don't know whether it came from an agent of that company, however, we do know that edit came from someone with access to their network," he wrote on the Wikipedia Scanner site.
A spokesperson for Wikipedia said the tool helped prevent conflicts of interest.
"We really value transparency and the scanner really takes this to another level," they said.
"Wikipedia Scanner may prevent an organisation or individuals from editing articles that they're really not supposed to."
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