Finance Minister and DUP deputy leader Peter Robinson praised Mr Paisley jnr for taking the "right decision" to quit the Executive.
"Recent media coverage in relation to Ian Paisley jnr has acted as a distraction from the important business of the Executive," he said.
"I believe Ian Paisley jnr has taken the right decision for the right reason. In drawing this particular chapter to a close I think it is important to record that in the last 10 months Ian Paisley jnr has made a significant contribution to both the Office of the First and Deputy First Minister and to the work of the wider Executive in often difficult personal circumstances."
However, Traditional Unionist leader Jim Allister, whose party polled well in last week's council election, said: "The fundamental problem is not just flawed personalities but flawed policies - particularly the policy of having IRA/Sinn Féin at the heart of government."
Developer Seymour Sweeney said: "Ian Paisley jnr is an extremely diligent politician who always works very hard for both his constituents and for projects he believes in."
Sinn Féin's Daithi McKay suggested Mr Paisley faced further troubles. "This is certainly not the end of it for Ian Paisley jnr," he said. "There are still a number of questions that he needs to answer in relation to the Giant's Causeway and other developments. All MLAs have a responsibility to act in a way that is beyond reproach."
SDLP North Antrim Assembly member Declan O'Loan said: "Questions surrounding Mr Paisley jnr's conduct will not go away as a result of his resignation. In fact, it will add to the growing pressure on his father who has been closely involved in so many of these matters including his employment as a Westminster researcher, his lobbying on land development and the rental of office premises from another family member."
David Ford claimed Ian Paisley jnr's behaviour had "severely damaged the credibility of the Executive. However, the questions being asked relate to his behaviour as an MLA," he added. "This would suggest he must resign as a MLA too."
Dr Peter Doran of the Green Party said: "The junior Minister's image threatened irreparable damage to the Assembly. Some people bring joy wherever they go - some people bring joy when they go."
Northern Secretary Shaun Woodward said: "On the public front it is obviously a matter for the DUP ... the Executive and Assembly. But on a private front I think one also has to acknowledge that, for the Paisley family, it is a very difficult time."
TIMELINE: events leading to resignation
April 2000: The visitor centre at the Giant's Causeway, which attracts 500,000 people a year, is burned down. It is replaced by a temporary structure.
September 10th, 2007: DUP Environment Minister Arlene Foster announces to the Assembly that she was of a mind to approve Mr Sweeney's plans for a visitors' centre development on his own land near the Giant's Causeway.
September 11th, 2007: Ms Foster says it is "rubbish" to suggest that she was influenced in her statement by Mr Sweeney's membership of the DUP.
September 19th 2007: Ian Paisley jnr confirms that he and his father had lobbied in 2005 for a drift net licence on behalf of a fisherman whose crew included Mr Sweeney and two of his relatives.
November 1st: The Belfast Telegraph claims to have documents which give details of 13 occasions when Mr Paisley was in contact with the British government in support of Mr Sweeney's company Seaport Investments over a five-year period up to 2006.
January 16th: Mr Paisley jnr admits he made "mistakes" in the controversy over his lobbying for constituency issues. But he also defends himself over claims he used the St Andrews talks to seek concessions from Tony Blair.
January 29th: Arlene Foster tells the Assembly she is refusing Seymour Sweeney's application for a private visitor centre at the Giant's Causeway. She says the proposal would have an adverse impact on the causeway's world heritage site status and would adversely affect the character of the area.
Tuesday, February 5th: Papers released show officials opposed the application, two months before the Ms Foster said she was of a mind to back it.
Wednesday, February 6th: It emerges that Ian Paisley jnr is being paid for doing Westminster research work for his father, as well as his MLA and junior minister salary of almost £63,000.
Thursday, February 14th: DUP failure to win Dromore council byelection partly blamed on bad publicity surrounding Ian Paisley jnr.
Monday, February 18th: It emerges that Dr Paisley and Ian Paisley jnr have paid £42,000 at taxpayers' expense to rent an office in Ballymena.
Money is paid to a company, in which Seymour Sweeney was formerly involved, and whose sole director is Mr Paisley's father-in-law, Jim Curry. - Dan Keenan