Em 2006 um sabido respondeu no r-help,

sciNotation <- function(x, digits = 1) {
    if (length(x) > 1) {
        return(append(sciNotation(x[1]), sciNotation(x[-1])))
    }
    if (!x) return(0)
    exponent <- floor(log10(x))
    base <- round(x / 10^exponent, digits)
    as.expression(substitute(base %.% 10^exponent,
                        list(base = base, exponent = exponent)))
}

plot(1:1000, axes = FALSE, type = "l", frame.plot = TRUE)
axis(1, at = axTicks(1), label = sciNotation(axTicks(1), 1))