documentclass{report}
numberwithin{equation}{section}
begin{document}

chapter{First}
begin{equation}
x^2 + y^2 = z^2
end{equation}
begin{equation}
x^3 + y^3 neq z^3
end{equation}

section{Next}
begin{equation}
a^2 + b^2 = c^2
end{equation}
begin{equation}
sqrt{-1} = - sqrt{-1}
end{equation}

end{document}

documentclass{report}
usepackage{amsmath}

renewcommand*{theequation}{%
  ifnumvalue{section}=0 %
    thechapter
  else
    thesection
  fi
  .arabic{equation}%
}
begin{document}

chapter{First}
begin{equation}
x^2 + y^2 = z^2
end{equation}
begin{equation}
x^3 + y^3 neq z^3
end{equation}

section{Next}
begin{equation}
a^2 + b^2 = c^2
end{equation}
begin{equation}
sqrt{-1} = - sqrt{-1}
end{equation}

end{document}