Chief executive Carrie Lam said that issue at Hung Hom Station platform has attracted widespread concern and is a matter of public safety.
Local reports have described the problem involving sections of rebar being cut to make it seem as though they had been screwed properly into couplers.
The independent and comprehensive investigation will examine the causes and assess the extent of the problems, she said. It will also review the Mass Transit Railway Corporation's works supervision system as well as the mechanism that the government uses to monitor and control such works to make recommendations to safeguard the quality of works and safety.
Former non-permanent judge of the Court of Final Appeal Justice Michael Hartmann will head the inquiry once approved by the chief executive in Council.
Lam said: "Justice Hartmann was the chairman of the Independent Expert Panel set up by the Government in 2014 to review the project delay relating to the Hong Kong section of the Guangzhou-Shenzhen-Hong Kong Express Rail Link, and is hence well versed in railway-related matters in Hong Kong. We hope that the commission can submit its report in about six months' time after its commencement of work, so that the truth can be unveiled as soon as possible.”
MTRC has rectified flaws; it took remedial action with the contractor after discovering the problem.