Vilamoura, Portugal, Oct 12, 2012 (AFP) - The 31-year-old slipped as he made his way off the opening hole and was only able to continue with a strapping on his left foot after receiving physiotherapy treatment.
The scare failed to disrupt his game though as he sank a 22-foot eagle putt on the 17th.
Reflecting on the freak accident Fisher said: "I didn't think anything of it at first and for two or three holes it was okay, but then it started to get really sore.
"The physio told me I was not doing any damage by playing on. It was uncomfortable for a while, I was feeling it again at the end and I'm just very relieved to get through."
In joint second were Scotland's Stephen Gallacher, who had shared the overnight lead with Fisher, and Bernd Wiesberger of Austria, after second rounds of 70 and 65 respectively.
One shot further back in a tie for fourth were Padraig Harrington and Fredrik Andersson Hed.
Fisher, who last won at the Irish Open in 2010, is aiming fror his fifth Tour success.
Among those missing the cut were Europe's Ryder Cup winning captain Jose Maria Olazabal and Darren Clarke, one of the favourites to succeed the Spaniard at Gleneagles in 2014.
Second round scores of the Portugal Masters at the Oceanico Victoria golf course on Friday (par 71, GBR & IRL unless stated):
132 - Ross Fisher 65 67
135 - Stephen Gallacher 65 70, Bernd Wiesberger (AUT) 70 65
136 - Fredrik Andersson Hed (SWE) 67 69, Padraig Harrington 69 67
137 - Christian Nilsson (SWE) 67 70, Michael Campbell (NZL) 68 69, Shane Lowry 67 70, Miguel Angel Jimenez (ESP) 69 68
138 - Jbe Kruger (RSA) 67 71, Richard Finch 70 68, Richard Green (AUS) 70 68, Jamie Donaldson 67 71, Mark Foster 71 67, Johan Edfors (SWE) 73 65
139 - Damien McGrane 70 69, Thomas Aiken (RSA) 68 71, Steve Webster 71 68, Danny Willett 70 69, Lee Slattery 69 70, Anthony Wall 68 71, Thorbjorn Olesen (DEN) 69 70, Gonzalo Fdez-Castano (ESP) 68 71, Rafael Cabrera Bello (ESP) 68 71
140 - Soren Kjeldsen (DEN) 69 71, Jean-Baptiste Gonnet (FRA) 72 68, David Howell 72 68, Marcel Siem (GER) 72 68, Peter Lawrie 73 67, Simon Dyson 72 68, Jamie Elson 71 69, Thomas Bjorn (DEN) 70 70, Markus Brier (AUT) 69 71, Pedro Figueiredo (POR) 70 70, Gregory Bourdy (FRA) 69 71, Henrik Stenson (SWE) 70 70
Selected
141 - Hennie Otto (RSA) 70 71, Keith Horne (RSA) 69 72
142 - Francesco Molinari (ITA) 71 71, Shaun Micheel (USA) 74 68, Matthew Zions (AUS) 70 72, Andrew Dodt (AUS) 72 70, George Coetzee (RSA) 69 73, Rich Beem (USA) 70 72
Missed cut
143 - James Kingston (RSA) 70 73, Jaco Van Zyl (RSA) 71 72
144 - Martin Kaymer (GER) 69 75, Richard Sterne (RSa) 73 71
145 - Tjaart Van Der Walt (RSa) 76 69
146 - Darren Fichardt (RSA) 74 72
148 - Darren Clarke 70 78
150 - Jose-Maria Olazabal (ESP)
151 - Edoardo Molinari (ITA) 71 80